From ilya@lisboa.ks.uiuc.edu Tue Jan 4 02:47:18 1994 Received: from lisboa.ks.uiuc.edu for ilya@lisboa.ks.uiuc.edu by www.ccl.net (8.6.4/930601.1506) id CAA12254; Tue, 4 Jan 1994 02:33:51 -0500 Received: by lisboa.ks.uiuc.edu (NX5.67d/NX3.0M) id AA13303; Tue, 4 Jan 94 01:33:47 -0600 Date: Tue, 4 Jan 94 01:33:47 -0600 From: Ilya Logunov Message-Id: <9401040733.AA13303@lisboa.ks.uiuc.edu> Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: CHEMISTRY@ccl.net Subject: Gaussian on HP Status: R Could somebody tell me where I can get the latest version of the Gaussian (g90 or g92) and how much it would cost? I intend to run Gaussian on HP 735 (or on cluster of HPs 735, if possible). Thus, any additional tips about compiling on this particular architecture will be also very much appreciated. Sincerely, ********************************************************* Ilya Logunov Theoretical Biophysics Group Department of Chemistry and Beckman Institute University of Illinois at U-C ilya@lisboa.ks.uiuc.edu ********************************************************* From scsupham@reading.ac.uk Tue Jan 4 06:47:12 1994 Received: from mail.rdg.ac.uk for scsupham@reading.ac.uk by www.ccl.net (8.6.4/930601.1506) id GAA12934; Tue, 4 Jan 1994 06:06:18 -0500 From: Received: from reading.ac.uk by mail.reading.ac.uk with SMTP (PP) id <23042-0@mail.reading.ac.uk>; Tue, 4 Jan 1994 11:05:58 +0000 Date: Tue, 4 Jan 94 11:05:56 GMT Message-Id: <2920.9401041105@scsscsc3> To: chemistry@ccl.net Subject: G92 and hydrogen bonds Cc: scsupham@reading.ac.uk Content-Type: X-sun-attachment Status: R ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 8 I have done some calculations with Gaussian92 with a good basis set on an isolated molecule and optimised the geometry which looks reasonable. However I have obtained 2 distances for C=N and C=O that are about 0.05A shorter than was observed in the crystal structure. However both the =N and =O were involved in intermolecular hydrogen bonds in the crystal. Is anybody aware of any work with Gaussian that shows that these types of bonds would be lengthened in the presence of hydrogen bonds? john upham (on behalf of Mike Drew here at Reading) John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: .signature X-Sun-Content-Lines: 3 John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 From X0ZHAO01@ULKYVX.LOUISVILLE.EDU Tue Jan 4 11:47:16 1994 Received: from ulkyvx.louisville.edu for X0ZHAO01@ULKYVX.LOUISVILLE.EDU by www.ccl.net (8.6.4/930601.1506) id LAA15107; Tue, 4 Jan 1994 11:43:59 -0500 Received: from ULKYVX.LOUISVILLE.EDU by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #3949) id <01H7A7EIDQB499DWUX@ULKYVX.LOUISVILLE.EDU>; Tue, 4 Jan 1994 11:42:25 EST Date: Tue, 04 Jan 1994 11:42:25 -0500 (EST) From: LIU JIANLING Subject: metal complexes To: chemistry@ccl.net Message-id: <01H7A7EIEJ8I99DWUX@ULKYVX.LOUISVILLE.EDU> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: X0ZHAO01 MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Status: R dear netters: can someone tell me how to start the MM calculation about transition metal complexes ? Specifically, which kind of force field is more suitable (MM2, MMX ... ?) When and where should I be careful , concerning the choices of "PARAMETERS" ? Thanks for your guidance to a NOVICE in this field ! From X0ZHAO01@ULKYVX.LOUISVILLE.EDU Tue Jan 4 11:47:16 1994 Received: from ulkyvx.louisville.edu for X0ZHAO01@ULKYVX.LOUISVILLE.EDU by www.ccl.net (8.6.4/930601.1506) id LAA15107; Tue, 4 Jan 1994 11:43:59 -0500 Received: from ULKYVX.LOUISVILLE.EDU by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #3949) id <01H7A7EIDQB499DWUX@ULKYVX.LOUISVILLE.EDU>; Tue, 4 Jan 1994 11:42:25 EST Date: Tue, 04 Jan 1994 11:42:25 -0500 (EST) From: LIU JIANLING Subject: metal complexes To: chemistry@ccl.net Message-id: <01H7A7EIEJ8I99DWUX@ULKYVX.LOUISVILLE.EDU> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: X0ZHAO01 MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Status: R dear netters: can someone tell me how to start the MM calculation about transition metal complexes ? Specifically, which kind of force field is more suitable (MM2, MMX ... ?) When and where should I be careful , concerning the choices of "PARAMETERS" ? Thanks for your guidance to a NOVICE in this field ! From CUNDARIT@MSUVX1.MEMST.EDU Tue Jan 4 14:47:23 1994 Received: from msuvx1.memst.edu for CUNDARIT@MSUVX1.MEMST.EDU by www.ccl.net (8.6.4/930601.1506) id OAA17031; Tue, 4 Jan 1994 14:00:29 -0500 Received: from MSUVX1.MEMST.EDU by MSUVX1.MEMST.EDU (PMDF V4.2-14 #3869) id <01H7AAKWNCF88WZ3U0@MSUVX1.MEMST.EDU>; Tue, 4 Jan 1994 13:02:02 CST Date: Tue, 04 Jan 1994 13:02:02 -0600 (CST) From: CUNDARIT@MSUVX1.MEMST.EDU Subject: MM and the metals To: chemistry@ccl.net Message-id: <01H7AAKWNCFA8WZ3U0@MSUVX1.MEMST.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Status: R A nice and recent review on the application of molecular mechanics to d- and f-block complexes can be found in the paper by Ben Hay (Coord. Chem. Rev. 1993, 126, 177 - 236). There are also refs to earlier reviews and work. Hay also gives good pointers on the development and choice of a force field. One of the projects in my group is the use of MM to design of specific chelates for f-block metal ions. Based on our research we have found the biggest hurdle is bond stretching parameters for metal-ligand bonds. In a preliminary work (Inorg. Chem. Acta 1993, 209, 101) we used MACROMODEL and a simple electrostatic model to describe the metal- ligand intrxn. This approach has the advantage that it is simple (i.e., cuts down on the number of parameters). Also, since the bonding in lanthanides is highly ionic it makes sense chemically. We have switched to a "traditional" approach (modeling M-L with a Hooke's law potential) similar to that in Hay's paper (Inorg. Chem. 1991, 30, 2876.) Another area of concern is the numerous torsional potentials involving the metal. One approach that has been used is to see all torsions about M-L bonds to zero; the geometry of the complex will then be determined by that which gives the most favorable non-bonded interactions. We use this approximation and can usually predict the tetrtiary structure of complexes quite well. One final area of concern is ligand-metal-ligand angles. As one goes to very high coordinatyion numbers these increase rapidly. This is further complicated by the fact that higher coordination geoms. often have inequivalent coordination sites (e.g., axial and equatorial in a trigonal bipyramid) each of which needs a different equilibrium angle and force constant. One approach I have seen is to replace the L-M-L potential for atoms with large coordination numbers with a potential that describes the 1,3-non-bonded interactions between the ligands. To our way of thinking, such an approach is simiar to the excellent (and in my opinion, underappreciated) points-on-a-sphere model, with which Kepert has done some seminal work on the coordination chemistry of transition metals . Finally, we typically assume that parameters which only involve the ligand do not change upon coordination. We are using the MM2 force field, as modified in Chem 3D+, since it is relatively quick, flexible (a true must), and provides a nice graphical user interface on a Quadra. These views are based on the specific needs of our MM/f-block research which is to model complexes quickly and give the experimental folks in the group some insight on ligand modifications which we can target. Any pointers,and experiences from other folks working on MM for metal complexes would be of interest to us. Tom Cundari Asst. Professor Dept. of Chemistry Computational Inorganic Chemistry Lab Memphis State University Memphis, TN 38152 phone: 901-678-2629 fax: 901-678-3447 From shen@phoenix.cs.uga.edu Tue Jan 4 16:47:23 1994 Received: from phoenix.cs.uga.edu for shen@phoenix.cs.uga.edu by www.ccl.net (8.6.4/930601.1506) id QAA20863; Tue, 4 Jan 1994 16:06:09 -0500 Received: by phoenix.cs.uga.edu (4.1/25-eef) id AA28562; Tue, 4 Jan 94 16:03:48 EST Date: Tue, 4 Jan 94 16:03:48 EST From: Mingzuo Shen Message-Id: <9401042103.AA28562@phoenix.cs.uga.edu> To: chemistry@ccl.net Subject: What are the "Dow"s and what are the "Du Pont"s ??? Hi all, In newspapers, magazines, advertisements, etc. I hear Dow. There are a lot of "Dow" chemical companies. Similarly, there are Du Pont . Exactly how many Du Pont companies are there? I thought somedoby who is familiar with the U.S. chemical industry may be willing to set me straight. Or even people from one of the chemical companies whose name bear "Dow" or "Du Pont". [Yes, I am interested because I want to investigate job prospects.] Thanks in advance for your time. Pointers where I may find information on all chemical and pharmaceutical companies are helpful too. Email and posts to this list are OK. Mingzuo Shen From jtgolab@amoco.com Tue Jan 4 19:47:21 1994 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.6.4/930601.1506) id TAA22271; Tue, 4 Jan 1994 19:21:05 -0500 Received: by interlock.amoco.com id AA10044 (InterLock SMTP Gateway 1.1 for chemistry@ccl.net); Tue, 4 Jan 1994 18:20:59 -0600 Received: by interlock.amoco.com (Internal Mail Agent-3); Tue, 4 Jan 1994 18:20:59 -0600 Received: by interlock.amoco.com (Internal Mail Agent-2); Tue, 4 Jan 1994 18:20:59 -0600 Received: by interlock.amoco.com (Internal Mail Agent-1); Tue, 4 Jan 1994 18:20:59 -0600 From: jtgolab@amoco.com (Joe Golab) Message-Id: <9401041820.ZM19091@unknown.zmail.host> Date: Tue, 4 Jan 1994 18:20:28 -0600 X-Mailer: Z-Mail (2.1.5 20sep93) To: chemistry@ccl.net Subject: Company Confusion This is a good question ... about Dow, DuPont, etc. I am employed by Amoco Chemical Company and I can respond about how it works. To all the MBA'd scientists/engineers/technicians out there ... if I do not use the absolutely correct business terms for what I mean, I consider myself lucky so don't bother to flame me. Amoco Chemical Company is a wholly owned subsidiary of Amoco Corporation. Other subsidiaries of the corporation are: Amoco Production, Amoco Oil, and Amoco Technology. For example, Amoco Oil refines crude oil and sells it as gasoline at those Amoco stations you might see on the road. Each company is lead by the strategic direction/mission of the corporation. On the other hand, each company has its own president and board of executive officers who are directly responsible for the day to day running of the company and ultimately on its "return on investment" to the corporation. Amoco Chemical has annual sales in the billions of dollars (American). The Chemical company is in turn split up into six distinct business units. Each of these is tied to a major product line and are pretty autonomous (although their strategies follow the company's general mission). For example, one of our business units, "Fiber and Films" recently acquired Phillips Fiber and Fabric. I know that (to the uninitiated) this reads like a lot of management overhead but in reality Amoco is a pretty flat organization. Amoco has two major research centers one in Naperville (Illinois, USA); the other in Tulsa (Oklahoma, USA). The one in Tulsa is pretty much a computer/geophysics shop and the major "tenant" is Production. The Naperville center is much more what one would think an R&D center is all about; Chemical, Oil, and Technology each have a building on site (or campus) and a bunch of PhDs work here. Much of the work is application driven and improvement oriented, although "new product" research is done. The people who work for Amoco at headquarters (in downtown Chicago) don't do any R&D (in the classical sense of the term) and are mainly business types, i.e. executive officers, accountants, marketeers, etc. As a computational chemist, my job function is fairly new here. My major task is to do what is necessary (within a budget) to provide quick, efficient, and effective access to theoretical methods that provide practical guidance for experimental work that is either too expensive, "dangerous", etc. This means that I work with non-theoreticians for the most part - other chemists who speak the "language/company lingo" of years of experimental work on company issues - as part of a problem-solving team. This means that most of what comes out of my mouth is "so much gobbeldy-gook" to them (although some theorists have told me that as well) and I end up translating "the molecule is moving according to its normal mode vector" into recognizable English (it's vibrating for cripes sake!). For example, telling people that a transition state has "one and only one negative eigenvalue in its Hessian" will make you _think_ that you are doing a great job until an experimentalist asks you what equipment s/he has to buy to test for "the negative ion value". BTW, I don't mean to imply that when you get to industry your "research days" are over; I do mean to imply that an industrial scientist/engineer/technician does work that is somehow related to the overall mission of the company and impacts the "bottom line" in a positive manner. Over time, I have found that one naturally picks projects that allow some research while doing either of the former. For job searching assistance, here is my advice (for what it is worth). At Amoco, the corporation solicits job applications. This means that if you send a scientist at Amoco your resume, s/he will most likely forward it to the appropriate HR (human resources) person at corporate. You should include a (single) page in addition to your resume, emphasizing why you can make a contribution to the company's R&D program (for example). Mention any unique (in your opinion) capabilities you have and how they might fit a (perceived) need in the company. I admit that this means you will have to read about the company or talk to someone "inside" but if its a job you want its worth it. Speaking as an industrial chemist, the work is challenging and enjoyable. At the risk of inviting a BUNCH of Email I will not have time/patience to read, I invite inquiries for more information. Good Luck! DISCLAIMER: All of this stuff is an opinion of my own conceiving. Any resemblance to company policy is entirely coincidental and completely in the mind of the reader. -- :Joe jtgolab@amoco.com