From AHOLDER@VAX1.UMKC.EDU Tue Jan 26 01:20:59 1993 Date: 26 Jan 1993 07:20:59 -0600 (CST) From: AHOLDER@VAX1.UMKC.EDU Subject: Semiempirical references To: chemistry@ccl.net Message-Id: <01GTYSPK5VFM8WW6QG@VAX1.UMKC.EDU> Greetings Netters! As Joe Leonard requested, following are the references I collected for the AMPAC 4.0 manual for the presently implemented semiempirical methods. SAM1 is not included, as the paper has not yet made it to publication. Michael Dewar has submitted it to Tetrahedron and it should be appearing soon. Andy =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 315 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= MNDO: M.J.S. Dewar, W. Thiel, J. Am. Chem. Soc. 99, 4899 (1977). MNDO Elemental Parameter Sets: Al L.P. Davis, R.M. Guidry, J.R. Williams, M.J.S. Dewar, H.S. Rzepa, J. Comp. Chem. 2, 433, (1981) B M.J.S. Dewar, M.L. McKee, J. Am. Chem. Soc. 99, 5231 (1977). Be M.J.S. Dewar, H.S. Rzepa, J. Am. Chem. Soc. 100, 777 (1978). Br M.J.S. Dewar, E.F. Healy, J. Comp. Chem. 4, 542 (1983). C M.J.S. Dewar, W. Thiel, J. Am. Chem. Soc. 99, 4907 (1977). Cl (a) M.J.S. Dewar, M.L. McKee, H.S. Rzepa, J. Am. Chem. Soc. 100, 3607 (1978). (b) M.J.S. Dewar, H.S. Rzepa, J. Comp. Chem. 4, 158 (1983). F M.J.S. Dewar, H.S. Rzepa, J. Am. Chem. Soc. 100, 58 (1978). Ge M.J.S. Dewar, E.F. Healy, G.L. Grady, Organometallics 6, 186 (1987). H M.J.S. Dewar, W. Thiel, J. Am. Chem. Soc. 99, 4907 (1977). Hg M.J.S. Dewar, G.L Grady, K.M. Merz, J.J.P. Stewart, Organometallics 4, 1964 (1985). I M.J.S. Dewar, E.F. Healy, J.J.P. Stewart, J. Comp. Chem. 5, 358 (1984). N M.J.S. Dewar, W. Thiel, J. Am. Chem. Soc. 99, 4907 (1977). O M.J.S. Dewar, W. Thiel, J. Am. Chem. Soc. 99, 4907 (1977). P M.J.S. Dewar, M.L. McKee, H.S. Rzepa, J. Am. Chem. Soc. 100, 3607 (1978). Pb M.J.S. Dewar, M.K. Holloway, G.L. Grady, J.J.P. Stewart, Organometallics 4, 1973 (1985). S M.J.S. Dewar, C. H. Reynolds, J. Comp. Chem. 7, 140 (1986). Si M.J.S. Dewar, E.F. Healy, J.J.P. Stewart, J.E. Friedheim, G.L. Grady, Organometallics 5, 375 (1986). Sn M.J.S. Dewar, G.L. Grady, J.J.P. Stewart, J. Am. Chem. Soc. 106, 6771 (1984). Zn M.J.S. Dewar, K.M. Merz, Organometallics 5, 1494 (1986). MNDOC: W. Thiel, J. Am. Chem. Soc. 103, 1413 (1981). MINDO/3: M.J.S. Dewar, R.C. Bingham, D.H. Lo, J. Am. Chem. Soc. 97, 1285 (1975). AM1: M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, J. Am. Chem. Soc. 107, 3902-3909 (1985). AM1 Elemental Parameter Sets: Al M. J. S. Dewar, A. J. Holder, Organometallics 9, 508 (1990). B M.J.S. Dewar, C. Jie, E.G. Zoebisch, Organometallics 7, 513 (1988). Br M.J.S. Dewar, E.G. Zoebisch, J. Mol. Struct. (Theochem) 180, 1 (1988). C M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985). Cl M.J.S. Dewar, E.G. Zoebisch, J. Mol. Struct. (Theochem) 180, 1 (1988). F M.J.S. Dewar, E.G. Zoebisch, J. Mol. Struct. (Theochem) 180, 1 (1988). Ge M.J.S. Dewar, C. Jie, Organometallics 8, 1544 (1989). H M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985). Hg M. J. S. Dewar, C. Jie, Organometallics 9, 1547 (1989). I M.J.S. Dewar, E.G. Zoebisch, J. Mol. Struct. (Theochem) 180, 1 (1988). N M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985). O M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985). P M.J.S. Dewar, C. Jie, J. Mol. Struct. (Theochem) 187, 1 (1989). S M. J. S. Dewar, Y.-C. Yuan, Inorganic Chemistry 29, 3881 (1990). Si M.J.S. Dewar, C. Jie, Organometallics 6, 1486 (1987). Sn M. J. S. Dewar, E. F. Healy, D. R. Kuhn, A. J. Holder, Organometallics 10, 431 (1991). Zn M.J.S. Dewar, K.M. Merz, Organometallics 7, 522 (1988). AM1-SM1, AM1-SM1a: C. J. Cramer, D. G. Truhlar, J. Am. Chem. Soc 113, 8305, 9901 (1991). AM1-SM2: C. J. Cramer, D. G. Truhlar, Science 256, 213 (1992). PM3: J. J. P. Stewart, J. Comput.Chem. 10, 209 (1989). PM3 Parameter Sets: J. J. P. Stewart, J. Comput.Chem. 10, 221 (1989). J. J. P. Stewart, J. Comput.Chem. 12, 320 (1991). PM3-SM3: C. J. Cramer, D. G. Truhlar, in press, (1992). From watanabe@tammy.harvard.edu Tue Jan 26 07:57:08 1993 Date: Tue, 26 Jan 93 12:57:08 -0500 From: watanabe@tammy.harvard.edu (Masa Watanabe) Message-Id: <9301261757.AA08382@tammy.harvard.edu> To: chemistry@ccl.net Subject: Solvation Free Energy Dear Netters, I'm looking for some references about solvation free energies of organic molecules in water. Anybody know good references (experimental or theoretical) to look at? Especially alcohol molecules in water. Hopefully, the reference has list of large numbers of different molecules. Thank you, Masa Watanabe Department of Chemistry Harvard University watanabe@tammy.harvard.edu From hogue@mosquito.den.mmc.com Tue Jan 26 04:47:19 1993 Date: Tue, 26 Jan 93 11:47:19 MST From: hogue@mosquito.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9301261847.AA03398@mosquito.den.mmc.com> To: chemistry@ccl.net Subject: Davidson optimization algorithm The GEOMOS program from QCPE refers to an optimization algorithm by Davidson. Can anyone give me a reference? Thanks Pat Hogue From jkl@ccl.net Tue Jan 26 09:43:18 1993 From: Jan Labanowski Date: Tue, 26 Jan 1993 14:43:18 -0500 Message-Id: <199301261943.AA01965@krakow.ccl.net> To: chemistry@ccl.net Subject: Searching CCL archives and DEC product info 2 announcements from your List-jockey: 1) To all you DEC fans: Digital Equipment Corp. has an anonymous ftp and e-mail service which distributes the information about DEC products/tests/etc. You can retrieve the info on how to get this information from CCL archives: Via ftp: ftp www.ccl.net (or ftp 128.146.36.48) Login: anonymous Pass: your_email-address ftp> cd /pub/chemistry/dec-alpha ftp> ascii ftp> get dec-info ftp> quit (By the way, DEC does not pay me anything...) or via e-mail by sending: send ./dec-alpha/dec-info from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET ------------------------- 2) After initial euphoria with searching Computational Chemistry List, most of you might have forgotten that there is a way to search CCL archives. For example, you want to find the files and messages which deal with MM2 parameters. So you send a query: 2 /MM2/ /parameter/ 1 & 2 to chemistry-search@ccl.net and the answer will be forwarded to your mailbox. In this example: 2 --- you have 2 search expressions: "MM2" and "parameter". 1 & 2 --- you want the files which have "MM2" AND "parameters" to be found. The complete information about chemistry-search is given in the file help.search in CCL archives. To get the file, send a message send help.search from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET or ftp it from the anonymous ftp on www.ccl.net as /pub/chemistry/help.search Jan Labanowski Ohio Supercomputer Center jkl@ccl.net From DSMITH@uoft02.utoledo.edu Tue Jan 26 10:08:30 1993 Date: Tue, 26 Jan 1993 15:08:30 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: Solvation Free Energy To: watanabe@tammy.harvard.edu Message-Id: <01GTZ8WGKMJQ000X8S@UOFT02.UTOLEDO.EDU> You might look at: 1. Smith, D. A.; Vijayakumar, S. Tetrahedron Lett. 1991, 32, 3617-3620. 2. Still, W. C., et al., J. Am. Chem. Soc. 1990, 112, 6127-6129. (There was a follow-up to this in JACS, but I don't have that reference handy.) I would also like to see a summary of responses if possible. Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From mbasd@seqnet.daresbury.ac.uk Tue Jan 26 20:03:35 1993 From: "A. Sheppard" Date: Tue, 26 Jan 93 20:03:35 GMT Message-Id: <26702.9301262003@s-crim1.dl.ac.uk> To: chemistry@ccl.net Subject: XWD->Mac conversion... Dear Netters, A few people suggested I post the following report, which I hope you will find useful. I have used the described techniques successfully to produce many a successful slide. I'd be interested in your comments. Ideas on a similar protocol for Unix->PC (Windows) picture conversion would be welcome. Andy mbasd@seqnet.dl.ac.uk ========================================================================== XWD -> MacPICT Picture Conversion ================================= A.Sheppard, 26/1/93 Introduction ============ This report describes a reliable and highly successful method of taking the output of the "xwd" program on the Evans & Sutherland ESV workstation and converting it to a PICT file suitable for viewing and editing in the more friendly environment of a Macintosh. This procedure was developed initially for viewing the output from the Sybyl molecular modelling program (Tripos Associates, St. Louis, MO, USA) on a Macintosh, but may of course be used for any 'xwd' picture. In addition, this method should allow conversion of the output from any X graphics workstation (e.g. Iris, Sun,...) to a Macintosh PICT file. Programs and Connections required ================================= ESV side: 1. xwd program (part of the standard OS release on the ESV) 2. kermit program (part of the standard OS release on the ESV) 3. compress program (part of the standard OS release on the ESV) 4. Serial or Ethernet connection from ESV to Macintosh. Macintosh side: 1. Colour Macintosh (8 bit colour minimum), preferably with >8 MB RAM and hard disk. 2. kermit or other terminal emulation program supporting the kermit file transfer protocol. [optionally, other file transfer protocols (e.g. FTP etc., may be used if preferred] 3. MacCompress or other program allowing decompression of Unix ".Z" files. 4. Imagery (this must be version 1.8 or greater to work with ESV ".xwd" files. Program memory partition should be set to as high a value as possible (e.g. 5000 K) 5. Colour painting program to view/edit results, e.g. MacCheese. (the Kermit, MacCompress and Imagery programs are available from many Mac bulletin boards and archives) Procedure ========= 1. On the ESV, display the X window containing the picture to be converted. 2. In a separate xterm window, type xwd -out test.xwd [RETURN] (where "test.xwd" is the filename for the picture). 3. Move the mouse arrow into the window containing the picture: the arrow should change to a "+". Click the left mouse button: a bell will ring followed by another bell to indicate completion. A file "test.xwd" should appear in the directory listing. Depending on the graphics window size, the file may be between 0 and several megabytes in size. A 400x400 pixel window will give a ".xwd" file 640106 bytes in size. 4. Type compress test.xwd [RETURN]. This will compress the file to make transfer to the Macintosh faster. The file test.xwd will be replaced in the directory listing by the file "test.xwd.Z" - the ".Z" indicates it is a compressed Unix file. The size of this file will depend on how much detail and how much empty space there was in the original ".xwd" file. In general, the less empty space, the bigger the ".Z" file. 5. On the Macintosh, establish the ESV-Mac connection by starting the file transfer program (e.g. kermit) and login. Make sure the kermit parameters are set to BINARY transfer protocol in the Macintosh program. 6. Move to the directory containing the test.xwd.Z file. type: kermit [RETURN] set file type binary [RETURN] send test.xwd.Z Start file transfer to the Macintosh by choosing "Receive file..." from the Macintosh File menu (this may vary from program to program). When transfer is complete, type: exit [RETURN] No more work on the ESV side is required. Logoff from the ESV and quit from terminal emulator. 7. Start the MacCompress program and choose "Decompress file..." from the "File..." menu - first make sure you have enough disk space to store the decompressed file! Select the "test.xwd.Z" file and press RETURN to decompress it. The ".Z" file will be replaced by the file "test.xwd". Quit from MacCompress (the ".xwd" extension will tell the Imagery program that a ".xwd" format file is to be processed). 8. Start the Imagery program. Select "PICT2" output and wait until conversion is complete. A file called "test.xwd.PICT" will be produced. Imagery quits automatically. 9. View/edit the "test.xwd.PICT" file using a colour painting program such as MacCheese or Photoshop. ========================================================================== From SHAUN%JASON.DECNET@relay.the.net Tue Jan 26 10:58:48 1993 Date: 26 Jan 1993 16:58:48 -0600 (CST) From: "Shaun D. Black" Subject: Summary of D-glucofuranose question To: chemistry@ccl.net Message-Id: <01GTZCSQ4BEQ000RLJ@nic.the.net> Dear CCLers, I have had a number of useful responses to my question on the existence of D-glucofuranose and associated energetic considerations. These are summarized below, with a bit of editorial comment included in brackets ([]). I hope some find this of use and of interest. -Shaun ORIGINAL QUESTION... ...Perhaps someone 'in the know' would be kind enough to enlighten me. That is, D-glucopyranose is always represented to be the most stable form of glucose (dextrose). However, what about D- glucofuranose? I've done some crude Hudson-type calculations, but was never able to convince myself that the furanose form was not unstable and that it should exist, probably; but, I've never seen it described. What's the real story? Enlightenment appreciated. SUMMARY... =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ITEM 1: From: caldwell@utdallas.edu (Richard A. Caldwell) 1/20/93 Suttie, "Introduction to Biochemistry," Holt, Rinehart, and Winston, New York, 1972, p 24, says: The ... furanose ring form of glucose is a less stable form and only a very small amount is present in the equilibrium mixture. There are, however, appreciable amounts of the furanose form present in the equilibrium solution of galactose and some of the rarer hexoses. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ITEM 2: From: mes@atlas.chemistry.uakron.edu (Mary Ellen Scott) 1/20/93 I'm not in the know, but I work with sugars. I have seen proton and carbon 13 NMR data that give ratios of pyranose, furanose, cyclic and I think hydrated forms of aldo and keto sugars. Are you determining stability by heat of formation? I have done Mopac calculations on alpha/beta glucose pyranose form but not furanose. What I would like to determine is the amount of acyclic form of fluorinated glucose derivatives vs glucose. If you have any suggestions please email. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ITEM 3: From: toni@athe.wustl.edu (Toni Kazic) 1/20/93 ...what is a Hudson calculation? ... [Some simple 'wysiwyg' rules to semi- quantitatively assess the stability of sugar conformers . E.g., axial -OH gets 1 'demerit', axial -CH2OH gets 2 demerits, axial -CH2OH and axial C-1 or 3 OH get 2.5 demerits, and 3 clustered O torsionally along C1,2 gets 2.5 demerits; in addition to the classical 'most positive optical rotation is the alpha anomer'.] =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ITEM 4: From: rwoods@biop.ox.ac.uk (Bob Woods) 1/21/93 A quick check in "Carbohydrate Chemistry. Monosaccharides and their Oligomers" by H.S.El Khadem, Academic Press, 1988 shows: Composition of Aqueous Solutions of D-Aldoses at Equilibrium ------------------------------------------------------------ Aldose total % pyranose total % furanose ------------ ---------------------- ---------------------- Allose 87 8.5 Altrose 67 33.0 Glucose 100 <0.3 Mannose 100 0.0 Gulose 78 22.0 Idose 75 25.0 Galactose 93 7.0 Talose 69 31.0 Ribose 80 20.0 Arabinose 97 4.5 Xylose 99.5 <0.5 Lyxose 98.0 2.0 ____________________________________________________________ I think you have raised a very interesting question; however, I am not aware of a suitable explanation of the variations. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ITEM 5: From: nauss@wrair-emh1.army.mil (Jeff Nauss) 1/21/93 As an addendum to Shaun Black's request for information about glucofuranose, I have a small project on-going concerning a molecular dynamics simulation of galactofuranose. I would also be interested in experiences others have had with modeling carbohydrates and especially furanose forms. I have quite a bit already on ribose and deoxyribose but virtually nothing on any other furanose. Any suggestions on useful carbohydrate-oriented force fields? =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ITEM 6: From: WTWINTER@SUVM.acs.SYR.EDU (Bill Winter) 1/21/93 I believe that Adam Allerhand from Univ Indiana published NMR results in the 1970's confirming the coexistence of a small percentage of glucofuranose in the equilibrium mixture in D2O. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | Bitnet: shaun%jason.decnet@thenic.bitnet = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=