From owner-chemistry@ccl.net Thu Feb 15 05:07:00 2007 From: "James Robinson James.Robinson,,prosonix.co.uk" To: CCL Subject: CCL: frequency Message-Id: <-33610-070215044848-3282-gl69Iuwl/7JvsYOAvDJ0tg:-:server.ccl.net> X-Original-From: "James Robinson" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 15 Feb 2007 09:15:51 -0000 MIME-Version: 1.0 Sent to CCL by: "James Robinson" [James.Robinson\a/prosonix.co.uk] Hi, you should check basis sets and one should expect greater differences if one has used implicit solvation during calculations. JJ Robinson, UK -----Original Message----- > From: owner-chemistry[A]ccl.net [mailto:owner-chemistry[A]ccl.net] Sent: 15 February 2007 02:53 To: James Robinson Subject: CCL: frequency Sent to CCL by: "neeraj misra" [misraneeraj ~ gmail.com] I am getting a C-N stretching vibration at 2602cm-1(unscaled HF) and at 2347cm-1(unscaled B3LYP) in a substituted benzonitrile molecule,is that very strange???? please comment. thanks in advancehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Feb 15 06:25:00 2007 From: "Nuno Loureiro Ferreira nunolf-#-ci.uc.pt" To: CCL Subject: CCL: Experimental data: protein diffusion coefficients Message-Id: <-33611-070215060840-28852-kC3jADUAzy4UQ8MwUVg/HA-.-server.ccl.net> X-Original-From: "Nuno Loureiro Ferreira" Date: Thu, 15 Feb 2007 06:08:36 -0500 Sent to CCL by: "Nuno Loureiro Ferreira" [nunolf\a/ci.uc.pt] Hi * I'm trying to find experimental data values on translational diffusion coefficients (Dt) of proteins on methanol. Though I've done some research on the net, I was not successful. I only found out Dt values for proteins in aqueous solutions, which is expected since this is the natural environment of most of the proteins. Nonetheless, several studies were done on proteins in different chemical environments, namely when determining NMR structures. Do you people know of the existence of exp. Dt values for proteins in methanol? Cheers, Nuno From owner-chemistry@ccl.net Thu Feb 15 07:12:00 2007 From: "Ding Xunlei dingxunlei[A]gmail.com" To: CCL Subject: CCL: about counterpoise calculation Message-Id: <-33612-070215070627-18125-uQQQypgINDId3jiHpJLVUw]-[server.ccl.net> X-Original-From: Ding Xunlei Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Thu, 15 Feb 2007 13:07:51 +0800 Mime-Version: 1.0 Sent to CCL by: Ding Xunlei [dingxunlei]|[gmail.com] Dear All, I am doing a calculation on the binding energy of AB. I need to calculate the BSSE, so I use counterpoise. It was found that stable=opt must be used to get the most stable wavefunction for all the three: AB, A, and B. How can I read the stabled wavefunctions in counterpoise calculation? Otherwise, the energies for AB,A,and B in counterpoise calculation are totally wrong and the BSSE energy < 0, which is obviously wrong. Thank you very much! Best regards, Ding From owner-chemistry@ccl.net Thu Feb 15 09:07:01 2007 From: "Saman Alavi saman.alavi*nrc.ca" To: CCL Subject: CCL: about counterpoise calculation Message-Id: <-33613-070215090556-19856-9HGAgNGX9ipmoLHTCIgmKw]^[server.ccl.net> X-Original-From: Saman Alavi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=GB2312 Date: Thu, 15 Feb 2007 09:07:07 -0500 MIME-Version: 1.0 Sent to CCL by: Saman Alavi [saman.alavi[#]nrc.ca] Hi Ding, Have you accounted for the small geometrical relaxation of the A and B fragments in the complex compared to the free structures? See the following references to account for this correction: S. S. Xantheas, J. Chem. Phys. 104, 8821 (1996) or the reference below to show an application of this correction: S. Alavi and D. L. Thompson, J. Phys. Chem. A 108, 8801 (2004) regards, Saman Ding Xunlei dingxunlei[A]gmail.com wrote: > Sent to CCL by: Ding Xunlei [dingxunlei]|[gmail.com] > Dear All, > > I am doing a calculation on the binding energy of AB. > I need to calculate the BSSE, so I use counterpoise. > > It was found that stable=opt must be used to get the most stable wavefunction for all the three: AB, A, and B. > How can I read the stabled wavefunctions in counterpoise calculation? > Otherwise, the energies for AB,A,and B in counterpoise calculation are > totally wrong and the BSSE energy < 0, which is obviously wrong. > > Thank you very much! > > Best regards, > Ding> > > > > From owner-chemistry@ccl.net Thu Feb 15 10:14:00 2007 From: "Ding Xunlei dingxunlei]*[gmail.com" To: CCL Subject: CCL: about counterpoise calculation Message-Id: <-33614-070215101010-12672-DOWqUG5CRXFnaL53ml8LOQ]|[server.ccl.net> X-Original-From: Ding Xunlei Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Thu, 15 Feb 2007 16:11:31 +0800 Mime-Version: 1.0 Sent to CCL by: Ding Xunlei [dingxunlei|-|gmail.com] Dear Saman, Thank you for your suggestion! In my calculation, the BSSE correction is calculated as E(A/with basis of AB)+E(B/with basis of AB)-E(A/with basis of A)-E(B/with basis of B), and the geometry in AB is used for both A and B in the above calculation. Best regards! Ding ______________________________________________ ======= 2007-02-15 22:07:07 You have written: ======= > >Sent to CCL by: Saman Alavi [saman.alavi[#]nrc.ca] >Hi Ding, > >Have you accounted for the small geometrical relaxation of the A and B >fragments in the complex compared to the free structures? > >See the following references to account for this correction: >S. S. Xantheas, J. Chem. Phys. 104, 8821 (1996) > >or the reference below to show an application of this correction: >S. Alavi and D. L. Thompson, J. Phys. Chem. A 108, 8801 (2004) > >regards, >Saman > > >Ding Xunlei dingxunlei[A]gmail.com wrote: >> Sent to CCL by: Ding Xunlei [dingxunlei]|[gmail.com] >> Dear All, >> >> I am doing a calculation on the binding energy of AB. >> I need to calculate the BSSE, so I use counterpoise. >> >> It was found that stable=opt must be used to get the most stable wavefunction for all the three: AB, A, and B. >> How can I read the stabled wavefunctions in counterpoise calculation? >> Otherwise, the energies for AB,A,and B in counterpoise calculation are >> totally wrong and the BSSE energy < 0, which is obviously wrong. >> >> Thank you very much! >> >> Best regards, >> Ding> > > = = = = = = = = = = = = = = = = = = = = From owner-chemistry@ccl.net Thu Feb 15 10:49:01 2007 From: "Chris Moth chris.moth.:.vanderbilt.edu" To: CCL Subject: CCL: C Programming question Message-Id: <-33615-070214183258-28131-eehSQPooS8qklMXfOjaEPg%x%server.ccl.net> X-Original-From: Chris Moth Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 14 Feb 2007 16:36:07 -0600 MIME-Version: 1.0 Sent to CCL by: Chris Moth [chris.moth#,#vanderbilt.edu] If you are not averse to dabbling in C++, you might experiment with function templates: http://www.cplusplus.com/doc/tutorial/templates.html Joseph M Leonard jleonard42[]gmail.com wrote: > > Sent to CCL by: "Joseph M Leonard" [jleonard42=gmail.com] > I assume there are people reading CCL that are more > into the nuances of C than I have been. I've got a question > for these folks... > > Is there a function similar to sizeof(var) that returns the type > rather than the byte-size of the specified variable? I'm aware > of the stdarg stuff that lets me check whether an argument is > a particular type, but I'd like to be able to do something like > > #define func(x) func_fn(x,type(x)) > > where the daughter routine knows what type of variable has > been passed in. I've been doing a bit of googling using various > phrases, and nothing obvious has come back... > > Your help is greatly appreciated! > > Joe Leonard > jleonard42_+_gmail.comhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > From owner-chemistry@ccl.net Thu Feb 15 11:45:00 2007 From: "Jozsef Csontos jozsefcsontos[#]creighton.edu" To: CCL Subject: CCL: about counterpoise calculation Message-Id: <-33616-070215113959-27729-juQlEycSiwVxMFsImzly9A[*]server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 15 Feb 2007 10:39:37 -0600 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos..creighton.edu] Hi, maybe I missed something but if you use the equation below then the BSSE correction should be not greater than zero (of course, if your calculated energies are smaller than zero). So, nothing is wrong with that. Jozsef On Thu, 2007-02-15 at 16:11 +0800, Ding Xunlei dingxunlei]*[gmail.com wrote: > Sent to CCL by: Ding Xunlei [dingxunlei|-|gmail.com] > Dear Saman, > > Thank you for your suggestion! > > In my calculation, the BSSE correction is calculated as > E(A/with basis of AB)+E(B/with basis of AB)-E(A/with basis of A)-E(B/with basis of B), > and the geometry in AB is used for both A and B in the above calculation. > > Best regards! > > Ding > > > ______________________________________________ > > ======= 2007-02-15 22:07:07 You have written: ======= > > > > >Sent to CCL by: Saman Alavi [saman.alavi[#]nrc.ca] > >Hi Ding, > > > >Have you accounted for the small geometrical relaxation of the A and B > >fragments in the complex compared to the free structures? > > > >See the following references to account for this correction: > >S. S. Xantheas, J. Chem. Phys. 104, 8821 (1996) > > > >or the reference below to show an application of this correction: > >S. Alavi and D. L. Thompson, J. Phys. Chem. A 108, 8801 (2004) > > > >regards, > >Saman > > > > > >Ding Xunlei dingxunlei[A]gmail.com wrote: > >> Sent to CCL by: Ding Xunlei [dingxunlei]|[gmail.com] > >> Dear All, > >> > >> I am doing a calculation on the binding energy of AB. > >> I need to calculate the BSSE, so I use counterpoise. > >> > >> It was found that stable=opt must be used to get the most stable wavefunction for all the three: AB, A, and B. > >> How can I read the stabled wavefunctions in counterpoise calculation? > >> Otherwise, the energies for AB,A,and B in counterpoise calculation are > >> totally wrong and the BSSE energy < 0, which is obviously wrong. > >> > >> Thank you very much! > >> > >> Best regards, > >> Ding> > > > > > > = = = = = = = = = = = = = = = = = = = => > > -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Thu Feb 15 17:43:00 2007 From: "Adil R Zhugralin zhugrali{=}bc.edu" To: CCL Subject: CCL: Summary: Drawing TS for QST2 calculations Message-Id: <-33617-070215174143-9364-Yxe8yhqMaVjTJStLIrmSSw=server.ccl.net> X-Original-From: "Adil R Zhugralin" Date: Thu, 15 Feb 2007 17:41:40 -0500 Sent to CCL by: "Adil R Zhugralin" [zhugrali]_[bc.edu] Thanks to everyone who's answered my previous question. QUESTION: I'm trying to get 2 molecules to react to give me an adduct. Unfortunately, the molecules are big (overall ~100 atoms). In GaussView, I find, it is practically impossible to draw them such that the proper trajectory is maintained and at the same time get the labeling to be consistent. Any suggestions about how to do it? Any software that could assist in creating starting material MolGroups? Thanks in advance. ANSWERS: ------------------- You may try to combine the coordinates of the two reactants together and then use chemoffice(chem3d) to display and manipulate them. ------------------- I will often start from the adduct and work my way back. Build the adduct and then sever bonds to form the two reactants. GaussView allows you to move the entire "group" upon lengthening the bonds between the two reactants. Atom labeling may be a little more difficult if you want the software to automatically number. The times that I've set up QST2 calculations I've manually written the input files and then manually pasted in the atom coordinates (to correspond to the product) after running a simple AM1 calculation on the "transition state" to obtain the atom coordinates. ------------------- The simplest approach to this is to take one of the structures and transform it into the other without deleting any atoms. This will keep the atom ordering the same as OPT=QST2/3 requires. Then delete bonds and move atoms to get products or an estimate of the TS starting from the reactants. Read in the first structure. Then select New/Add to MolGroup to generate a connected view. Select the molecule and Copy from the Edit menu and paste it in the new view. Repeat for QST3. There is also a tool in GaussView which attempts to help you re-organize the atoms, looks like a chain on the icon. It have not tried it with 100 atoms so I would start the the mechanism above if possible and use chain if something gets confused, starting with 95+ of the atoms in the right order should make this easier. ------------------