From chemistry-request%!at!%server.ccl.net Wed Mar 1 12:34:54 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA05010 for ; Wed, 1 Mar 2000 12:34:53 -0500 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JMIOP5EYFM001XGA #at# trentu.ca> for chemistry #at# ccl.net; Wed, 1 Mar 2000 12:33:38 EST Date: Wed, 01 Mar 2000 12:37:24 -0500 From: elewars Subject: SAM1 SUMMARY To: chemistry %-% at %-% ccl.net Message-id: <38BD5553.A87FB87F $#at#$ trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Wed 2000 March 1 Here is the summary to my question about SAM1. I thank everyone who responded. EL --- The Question Wed, 2000 Feb 23 Hello, In 1993 the Dewar group announced the development of the SAM1 ("semi ab initio #1") method. I know the basic principles behind it, but would like to know: 1) What became of it? It does not seem to appear much in the literature. 2) Did computational chemists conclude it is not much better than AM1, and so let it fall into disuse? 3) I think it is offered in AMPAC; does any other package have it? Thanks EL ==== The Responses (#1--#5) #1 Subject: Re: CCL:SAM1 semiempirical method Date: Wed, 23 Feb 2000 19:23:18 -0500 (EST) From: Joe M Leonard To: elewars Semichem's AMPAC contains SAM/1 along with various other semi-empirical methods, and it's still a going concern. Tripos sells it commercially, but the development's done in KC, not StL. We've integrated it with our small/large molecule visualization software, FYI. Joe === #2 From: Thomas Heine To: elewars References: Hello, You could ask Slanina who published 1998 SAM1 results of fullerenes. Though they were not really good :) Z. Slanina et al., CPL 290:311, 1998. I don't know his exact address but he lives in Japan (Osaka I think) and has a webpage. Cheers, Thomas ============ #3 Re: CCL:SAM1 semiempirical method Date: Thu, 24 Feb 2000 10:10:01 -0500 From: Andrew T Pudzianowski Organization: Bristol-Myers Squibb To: elewars Dr. Lewars - I've been using SAM1 extensively for a few years now. It offers significant improvements over previous Dewar-style methodologies, especially in its performance with H-bonded systems. I've also had a chance to compare SAM1 results for isomer and conformer structures and energies directly with various ab initio and DFT results, the latter usually at levels like B3-LYP/6-31+G(d,p) or another augmented double-zeta basis with polarization functions, and have found near-quantitative agreement in most cases. On the other hand, SAM1 continues to share some notable failures with its MNDO and AM1 predecessors, and it has a fluke or two of its own. On the whole I'd say SAM1 represents some real progress in semiempirical methodology, but it isn't more widely used because it's currently available only in the commercial AMPAC software from Andy Holder's company, Semichem. Also, the rationale for not fully disclosing the parametrization of SAM1 in the open literature is that SAM1 is a unique feature of AMPAC, the sale of which is a source of funding for the continuing development of semiempirical methodologies in Holder's group. Because many chemists are reluctant to work with a methodology that has a significant unpublished component, I think this has also tended to limit both the use of SAM1 and dissemination of results. The latter aspect may be compounded by the possibility that, like yours truly, a lot of AMPAC users are employed in industry and can't publish the relevant results until patents and other competitive issues have been resolved. I think these factors have conspired to limit the exposure of SAM1 to the computational community, ultimately to the detriment of continued improvement of semiempirical methodologies, I'm afraid. Regards, Andrew Pudzianowski =============== #4 Hi EL, You asked about the SAM1 method: >I know the basic principles behind it, but would like to know: >1) What became of it? It does not seem to appear much in the literature. > >2) Did computational chemists conclude it is not much better than AM1, >and so let it fall into disuse? >3) I think it is offered in AMPAC; does any other package have it? Yes, it is offered in Ampac, and is continuing to be developed by Andy Holder's group (with Dewar's blessing, when he "passed the torch" to Andy). You can contact them at Semichem: http://www.semichem.com/ I believe you can also get AMPAC through Serena Software: http://www.serenasoft.com/ although I think they only provide an alternative interface. So far as SAM1, it does seem to be much better than AM1 in at least 2 respects; it includes d orbitals, so it has been parameterized to model some transition metal compounds, and it also provides more accurate vibrational frequencies than AM1 calculations. (Scaling is still required, but SAM1 frequencies are more accurate and much more consistent.) Parameterization of the metals has been a slow process, so only a few are available, and in fact the final "certified" SAM1 parameters for Fe were only released last year, hence not many publications yet. (In my own experience, SAM1 works much better for organometallic Fe complexes than it does for simple hydrates.) The improvement in frequency calculations has been published, see: A. J. Holder & R. D Dennington II, J. Mol. Struct. (THEOCHEM), 401(3), 207-18 (1997). I expect to see more published with SAM1 in the future, particularly as more transition metals are parameterized. EC --- Ernest Chamot Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 (630)637-1559 echamot _-at-_)chamotlabs.com http://www.chamotlabs.com/cl ============== #5 Colleagues, Several days ago the following questions were posed. Sorry it took me some time to respond. > In 1993 the Dewar group announced the development of the SAM1 ("semi ab > initio #1") method. > I know the basic principles behind it, but would like to know: > 1) What became of it? It does not seem to appear much in the literature. The SAM1 method is still under development in my Group at the University of Missouri-Kansas City. We are working on refining some additional parameters and have added some new computational algorithms (an improved CI (1) and a quadratically (to be published) convergent SCF procedure) to make the method tractable for open-shell transition metals. The references to the method currently extant in the literature are listed below. A major paper describing the full implementation and listing parameter values is in preparation. > 2) Did computational chemists conclude it is not much better than AM1, > and so let it fall into disuse? Actually, SAM1 performs better than AM1 in most cases for CHON and the halogens. We have parameters for Si, S, P that are better than AM1 as well, especially for hypervalent species. The TM parameters for Fe, Cu, and Zn are basically completed and others are underway. > 3) I think it is offered in AMPAC; does any other package have it? Currently Semichem's AMPAC is the only program in which it has been implemented, but we expect other vendors to put it in when the theoretical paper and parameters are published. References: ----------- (1) [CI paper] Liotard, D.L.; Holder, A.J. J. Chem. Inf. Comput. Sci. 1999, 39, 587. (2) [SAM1] Dewar, M. J. S.; Jie, C.; Yu, G. Tetrahedron 1993, 23, 5003. (3) [SAM1] Holder, A. J.; Dennington, R. D.; Jie, C. Tetrahedron 1994, 50, 627. (4) [SAM1] Holder, A. J.; Evleth, E. M. in Modeling the Hydrogen Bond; Smith, D. A.; American Chemical Society, Washington, DC, 1994; p 113. Regards, Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- UUUU UUU MMM MMKK KKKK CCCC | ANDREW J. HOLDER UU U MM MMK K CC CC | Assoc. Prof. of Comp./Org. Chemistry UU U MMM M MK KK CCC | Dept. of Chemistry UU U M MM MK KK CC CC | University of Missouri-Kansas City UUUUU MMM M MMKK KK CCCC | Kansas City, MO 64110 KK | holdera%!at!%umkc.edu K | (816) 235-2293, FAX (816) 235-6543 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- =============