From chemistry-request@server.ccl.net Sun Jun 18 20:37:14 2000 Received: from smtppop3.gte.net (smtppop3pub.gte.net [206.46.170.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA20915 for ; Sun, 18 Jun 2000 20:37:13 -0400 Received: from oemcomputer (1Cust219.tnt6.bos2.da.uu.net [63.22.117.219]) by smtppop3.gte.net with SMTP for ; id TAA3289245 Sun, 18 Jun 2000 19:34:24 -0500 (CDT) Message-ID: <001d01bfd985$87008820$09a0fea9@oemcomputer> From: "David Anick" To: Subject: Activation Barrier vs Stability Date: Sun, 18 Jun 2000 20:30:00 -0400 Dear CCL subscribers, I would be interested in opinions, examples, best guesses, references, or published data related to the following two questions. I will be happy to summarize responses. (1) I have a unimolecular "rearrangement" reaction for which I have computed state A ("reactant"), state B ("product"), and the T-state. All three are converged to nicely by optimization programs, with A and B being PES minima and the TS a 1st order saddle. The electronic energy of A is below that of the TS by 3 kcal/mol, but when I compute and add in the ZPE's, state A has slightly higher energy than the TS (by ~ 0.2 kcal/mol). State B is of considerably lower energy than either, even after ZPE corrections. What does this mean? Would the molecule quickly tunnel out of state A at 0 K? Can I consider A to be a stable (even if short-lived) state of the molecule, or must it be viewed as an unstable intermediate or transitional state? Would it be correct to use the energy difference between A and B, to talk about a Boltzmann distribution of a population into states A and B, or would it all be basically B? (2) Like (1) in that there is a unimolecular reaction A -> B, but now both A and B have energies below the TS (including the ZPE corrections). My question is, is there a ball park estimate for the temperature T at which A becomes unstable, in terms of the activation barrier (i.e. DG =3D G(TS) - G(A)). I'm open to opinions about how "unstable" should be defined, but an operational definition could be "half-life of A less than a minute". I think this comes down to predicting the pre- Arrhenius factor, and there will be a wide range answers depending on the reaction, but I wonder if anyone can offer gross generalizations, e.g. "small organic molecules for which such a rearrangement pathway exists, are typically unstable above temp DG/10kB", or the like. The DG's (with ZPE included) I'm looking at are between 2 and 10 kcal/mol, and the reactions involve the movement of 3 to 6 second row atoms. Thank you very much for taking the time to read this. Any and all responses will be much appreciated. Sincerely, David Anick MD PhD David.Anick@gte.net From chemistry-request@server.ccl.net Mon Jun 19 06:06:11 2000 Received: from fecit-gate.fecit.co.uk (firewall-user@[193.119.134.250]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA22937 for ; Mon, 19 Jun 2000 06:06:10 -0400 Received: by fecit-gate.fecit.co.uk; id LAA15836; Mon, 19 Jun 2000 11:11:06 +0100 Received: from suisei(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V5.0) id xma015822; Mon, 19 Jun 00 11:10:09 +0100 Received: from fecit.co.uk (NT11.fecit.co.uk [192.168.101.116]) by suisei.fecit.co.uk (8.6.9/8.6.9) with ESMTP id LAA24962; Mon, 19 Jun 2000 11:14:53 +0100 Message-ID: <394DF00D.B94D9949@fecit.co.uk> Date: Mon, 19 Jun 2000 11:03:57 +0100 From: Herbert Fruchtl Organization: Fujitsu European Centre for Information Technology X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: yunlong song CC: "CHEMISTRY@ccl.net" Subject: Re: CCL:about AM1 References: <20000617082155.BFHE361.fep2.online.sh.cn@cadd> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Yunlong, The result of a geometry optimization depends not only on the Hamiltonian, but also on the optimization algorithm, e.g., which (if any) Hessian update is used, maximum step length, etc.. If a barrier is crossed depends very much on the optimization method, and possibly on the exact starting point (if not to say luck). The optimizers generally used in quantum chemistry are guaranteed to find a local minimum (if they converge), not necessarily the global minimum, or the closest minimum to the starting structure, or whichever minimum you look for. If you want to compare the AM1 implementations, look at single-point energies. The optimizer is not part of the method. Both Gaussian and newer versions of MOPAC have several optimizers to choose from (Gaussian more so). HTH, Herbert yunlong song wrote: > > Dear CCLers, > I find that AM1 method in Gaussian 98 may be different from AM1 in MOPAC,because when I optimize the same molecule > with the two methods, I got different results.AM1 in G98 seems to be much effective ,in that it can overcome a large > energy barrier. I am interested to know which cause this difference.Can it be the implementation method that cause such > results? Can you tell me the difference about the same method in the two soft package? > Any information will be appreciated! > Thank you in advance! > From chemistry-request@server.ccl.net Mon Jun 19 10:42:15 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA24864 for ; Mon, 19 Jun 2000 10:42:09 -0400 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Mon, 19 Jun 2000 22:45:46 +0800 Sender: user@ccl.net Message-ID: <394E213E.341FFD46@iris.sipp.ac.cn> Date: Mon, 19 Jun 2000 22:33:50 +0900 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: proton transfer reaction Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello: Does anyone know the references or some compuational methods to get the kinetic parameters of the intramolecular or intermolecular proton transfer reaction in gas or solution. Thanks in advance. Regards, mao xiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Mon Jun 19 13:38:32 2000 Received: from prserv.net (out4.prserv.net [32.97.166.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA25951 for ; Mon, 19 Jun 2000 13:38:32 -0400 From: jmmckel@attglobal.net Received: from schubert ([32.101.104.137]) by prserv.net (out4) with SMTP id <2000061917381423900q9grqe>; Mon, 19 Jun 2000 17:38:16 +0000 Message-ID: <394E5A43.EA2@attglobal.net> Date: Mon, 19 Jun 2000 12:37:07 -0500 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 3.04 (WinNT; I) MIME-Version: 1.0 To: yunlong song CC: "CHEMISTRY@ccl.net" Subject: Re: CCL:about AM1 References: <20000617082155.BFHE361.fep2.online.sh.cn@cadd> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit yunlong song wrote: > > Dear CCLers, > I find that AM1 method in Gaussian 98 may be different from AM1 in MOPAC,because when I optimize the same molecule > with the two methods, I got different results.AM1 in G98 seems to be much effective ,in that it can overcome a large > energy barrier. I am interested to know which cause this difference.Can it be the implementation method that cause such > results? Can you tell me the difference about the same method in the two soft package? > Any information will be appreciated! > Thank you in advance! > > Dr yunlong song > ------------------- > songyunlong@163.net > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Dr. WSong, I have never had G94/G98 give different answers relative to MOPAC if the MOPAC optimization was done using EF, PRECISE and GNORM=0 keywords. I believe this problem was also discussed by Stewart and Boyd in (I believe) a JCompChem article. John McKelvey From chemistry-request@server.ccl.net Mon Jun 19 14:00:19 2000 Received: from smtp.engin.umich.edu (root@smtp.engin.umich.edu [141.213.75.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA26074 for ; Mon, 19 Jun 2000 14:00:19 -0400 Received: from umich.edu (sastry2.engin.umich.edu [141.212.137.85]) by smtp.engin.umich.edu (8.9.1a/8.9.1) with ESMTP id NAA17432 for ; Mon, 19 Jun 2000 13:48:37 -0400 (EDT) Message-ID: <394E5CF8.24FFDF99@umich.edu> Date: Mon, 19 Jun 2000 13:48:40 -0400 From: John Reply-To: jparm@umich.edu X-Mailer: Mozilla 4.72 (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: CCL: molecular chain dimensions Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Hello All, I'm conducting research on biological nanoscale composites. I have a situation where I know the connectivity of a molecular chain (sulfated fucose polymer), and would like to calculate the physical dimensions of the chain (average diameter for all of the various conformations) as well as, say, how many molecular chains may be bundled together to make a nano-scale fiber of known diameter. I was hoping that someone could recommend some references so that I could learn how to do this. Also I understand that there are computer programs that do these types of calculations, what would be an appropriate one? Thank you.