From owner-hyperchem@hyper.com Thu Aug 1 09:58:25 1996 From: Massimo Trotta Subject: dipolar moments To: CHEMISTRY@infomeister.osc.edu Date: Thu, 1 Aug 1996 12:21:01 +0200 (MET DST) Cc: hyperchem@hyper.com Dear all, I'm studying the dipolar moments of some organic molecules in the ground and first excited states using semi-empirical calculations (on Hyperchem 4.0) and I have a couple of question regarding those calculations: a) I decided to use ZINDO/1 as semiempirical method (available methods are CNDO, INDO, MINDO3, MNDO, AM1, PM3, ZINDO/1 and ZINDO/s), but the choice was not made on how appropriate is the method for evaluating dipolar moment. Am I doing right? is there any reason for choosing this or that SE method for the dipolar moment calculations? b) In evaluating the dipole moment in the excited state I select the option _Next Lowest_ in the SE option dialog box. Should I work with _Unrestricted Hartree Fox_ to get more accurate number or _Restrictes HF_ gives the same accuracy as well?. c) How can I display, in hyperchem or with some other software (freeware) the dipolar moments as spacial vectors overlapped on the molecules? Any indication is welcome. will summarize. massimo -- !==============================================================! ! Massimo Trotta ! ! Centro Studi Chimico Fisici sull'Interazione Luce Materia ! ! c/o Dept. of Chemistry ! ! V. Orabona, 4 I-70126 Italy ! ! e-mail: csilmt12@area.ba.cnr.it ! ! http://www.ba.cnr.it/~csilmt12 !==============================================================! _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 1 14:50:40 1996 Date: Thu, 1 Aug 96 11:25:27 -0400 From: polowin (Joel Polowin) To: tailkink@silicon.chem.QueensU.CA (Evan Vaughan) Subject: Re: Graphics cards Cc: hyperchem@hyper.com > Date: Wed, 31 Jul 96 18:21:43 EDT > From: tailkink@silicon.chem.QueensU.CA (Evan Vaughan) > > Hi! I was wondering what kind of graphics cards you recommend for using > with Hyperchem? Thanks! HyperChem does not make direct use of add-on hardware such as graphics accelerators; all of its drawing and printing functions are done through Windows. However, if you do have something like a graphics accelerator installed, then when HyperChem tells Windows to go and draw a picture, then Windows would relay the request to the accelerator. The result is an indirect improvement in performance. We do not have any specific recommendations for graphics cards; any of them should be fine. If anyone else on the mailing list can comment on the effects of an accelerator card on running HyperChem, I'd like to hear about it. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 1 15:35:44 1996 Date: Thu, 1 Aug 96 12:04:22 -0400 From: polowin (Joel Polowin) To: allin@helios.bph.ruhr-uni-bochum.de (Christoph Allin), hyperchem@hyper.com Subject: Re: Convergence Problem > Date: Wed, 31 Jul 1996 20:04:26 +0200 > From: allin@helios.bph.ruhr-uni-bochum.de (Christoph Allin) > > we try to minimize the structure of H2PO4 complexed with one Mg. Our intention > is to calculate the normal modes of this system. Therefore we are interested in > the well relaxed structure (very small gradient). We used the > following input data for the calculations (extract of the log file): > > Criterion of RMS gradient = 0.0010 kcal/(A mol) Maximum cycles = 120 > Starting HyperGauss calculation for IRIX 5.x versions 4.5 (Serial No. > 600-10000000) with 108 basis functions and 230 primitive Gaussians > > After a few days of calculation we have got the problem, that the gradient do > not reach a value smaller than 0.012 kcal/(A mol). We have read in the > reference manual, that by means of numerical round-off errors, there exists a > limit for the value of the RMS gradient of 0.001. But our result is still above > this limit. > > E=-527637.1875 Grad=0.013 Conv=NO(1 cycles 23 points) [Iter=1 Diff=0.00000] The structure has a shallow potential energy surface, and it appears that you have let it run only for between 1 and 2 optimization cycles out of a default maximum of 120 cycles. The simple answer is that the structure will probably need longer to optimize. I ran an optimization on this structure, as contructed by the model builder, with PM3, using the same gradient convergence criterion 0f .001 kcal/(A mol). The first optimization of 120 cycles brought the gradient down to about 0.016. When I optimized the structure a second time from that point, the first optimization cycle reduced the gradient to 0.007 but it was not until after 36 cycles (87 points) that the system converged with a gradient of 0.001. I would expect that the potential surface for _ab initio_ calculations, and the optimization pattern, would be similar. You did not mention which basis set(s) you are using. But you might find it more efficient to do a two-step optimization -- first with a small basis set, which will give you an approximate optimization relatively quickly, and then with a larger basis set to improve the accuracy. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 2 19:14:51 1996 Date: Fri, 2 Aug 96 17:10:57 -0400 From: polowin (Joel Polowin) To: Phillip Stafford , Jens Spanget-Larsen Subject: Re: Endothermic? Cc: hyperchem@hyper.com > Date: Mon, 29 Jul 1996 17:39:39 -0500 (CDT) > From: Phillip Stafford > > The CH3CN (Acetonitrile) reaction is endothermic, at least in my > experience in the lab. Most reactions I've run across using acetonitrile > get very cold immediately after the reaction begins. Er -- *which* acetonitrile reaction? I can easily imagine that, for example, the heat of solution might be negative. But that doesn't have much to do with the gas-phase proton affinity which was being modelled here. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 2 19:36:02 1996 Date: Fri, 2 Aug 96 16:44:59 -0400 From: polowin (Joel Polowin) To: Massimo Trotta , CHEMISTRY@infomeister.osc.edu Subject: Re: dipolar moments Cc: hyperchem@hyper.com > From: Massimo Trotta > Date: Thu, 1 Aug 1996 12:21:01 +0200 (MET DST) > > I'm studying the dipolar moments of some organic molecules in the > ground and first excited states using semi-empirical calculations > (on Hyperchem 4.0) and I have a couple of question regarding those calculations: > a) I decided to use ZINDO/1 as semiempirical method (available methods are > CNDO, INDO, MINDO3, MNDO, AM1, PM3, ZINDO/1 and ZINDO/s), but the choice was > not made on how appropriate is the method for evaluating dipolar moment. Am I > doing right? is there any reason for choosing this or that SE method for the > dipolar moment calculations? The advantage of ZINDO/1 is that it is parameterized for transition metals. For general work on organic compounds, you are probably better off using AM1 or PM3. For dipole calculations, AM1 is likely to give slightly better accuracy, on average. This may not be true for a particular set of molecules which are all rather similar but have some relatively minor structural differences. > b) In evaluating the dipole moment in the excited state I select the option > _Next Lowest_ in the SE option dialog box. Should I work with _Unrestricted > Hartree Fox_ to get more accurate number or _Restrictes HF_ gives the same > accuracy as well?. For closed-shell systems you should use RHF; for open-shell systems you should use UHF. Please note that "Lowest" and "Next Lowest" refer to the specified multiplicity -- for example, the lowest and second-lowest singlet state -- and not to all states. For a molecule whose ground state is a singlet, the first excited state is probably "Lowest" of multiplicity 3, not "Next Lowest" of multiplicity 1. > c) How can I display, in hyperchem or with some other software (freeware) > the dipolar moments as spacial vectors overlapped on the molecules? This cannot be done with current versions of HyperChem -- at least, not easily. I suppose that you could get the dipole vector from HyperChem by using the "dipole-moment-components" script command, or from a log file, and use those values to specify coordinates for the atoms in a diatomic molecule. One atom could be placed at coordinates in Angstroms given by the dipole components in Debyes, and the other atom at the coordinates multiplied by -1; the original molecule could be centred on the origin, and then the new diatomic molecule would show the dipole. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Aug 7 10:16:53 1996 From: Massimo Trotta Subject: Dipol moments II To: hyperchem@hyper.com Date: Wed, 7 Aug 1996 12:45:38 +0200 (MET DST) dear joel, thank you for the reply, on which I'd like to ask some more details: > > The advantage of ZINDO/1 is that it is parameterized for transition metals. > For general work on organic compounds, you are probably better off using > AM1 or PM3. For dipole calculations, AM1 is likely to give slightly > better accuracy, on average. This may not be true for a particular set > of molecules which are all rather similar but have some relatively minor > structural differences. I guess the last sentence refers to a general failure of SE methods. Am I wrong in thinking that methyl groups are not a minor difference? In particular I am looking to the family of methyl substituted Benzoqinones (from 1 to 4 substituting methyl groups). Using Zindo I found some differences among the various dipolar moments. > > > b) In evaluating the dipole moment in the excited state I select the option > > _Next Lowest_ in the SE option dialog box. Should I work with _Unrestricted > > Hartree Fox_ to get more accurate number or _Restrictes HF_ gives the same > > accuracy as well?. > > For closed-shell systems you should use RHF; for open-shell systems you > should use UHF. that means that UHF should be applied when the _Next Lowest_ option is selected. This matches with what I knew, but in the Reference manual of Vers. 4 (pag. 193) under the voice "spin pairing" is written: RHF: ................. This method is useful for open- and closed shells. This may be confusing (at least it was confusing for me). > Please note that "Lowest" and "Next Lowest" refer to the > specified multiplicity -- for example, the lowest and second-lowest > singlet state -- and not to all states. For a molecule whose ground > state is a singlet, the first excited state is probably "Lowest" of > multiplicity 3, not "Next Lowest" of multiplicity 1. > This must be the reason why when you choose _Next Lowest_ the multeplicity option is not available. Regarding the _Next Lowest_, is it possible to generate a grid for the total charge density? I tryed to do it via the _Contour Plot_ option, but it didn't work out. thank you massimo -- !==============================================================! ! Massimo Trotta ! ! Centro Studi Chimico Fisici sull'Interazione Luce Materia ! ! c/o Dept. of Chemistry ! ! V. Orabona, 4 I-70126 Italy ! ! e-mail: csilmt12@area.ba.cnr.it ! ! http://www.ba.cnr.it/~csilmt12 !==============================================================! _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Aug 7 12:12:14 1996 Date: Wed, 7 Aug 1996 13:15:15 +0100 (BST) From: patrick kane <94970459@tolka.dcu.ie> To: HChem User , HChem Supp , CCL Every Subject: HyperChem and Schakal Hi, I would be much obliged if anyone tell me if there is a file format which is compatible with both HyperChem and Schakal. Thank you in anticipation for your help. Regards, Paddy. Paddy Kane Dublin City University 94970459@tolka.dcu.ie --------------------------------------------- --------------------------------------------- _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Aug 7 14:23:32 1996 X400-Originator: Matthew.Harbowy@unilever.com Date: 07 Aug 1996 16:54:45 +0100 From: "Matthew Harbowy" To: "chemistry@infomeister.osc.edu" Cc: "hyperchem@hyper.com" (Return requested) Subject: Branched vs straight chain alkanes In the Handbook of Chem and Physics, it reports octane: -49.82 2,2,3,3,TMB: -53.99 My results for AM1 and MM+ show (Hyperchem 3.0 calculations) am1 mm+ exp octane -58.628 (6.448 s.e.) -49.82 2,2,3,3,TMB -40.155 (12.36 s.e.) -53.99 ------------- ---------- -------------- ------------ oct - tmb -18.473 -5.912 4.17 So, yes, it would seem that both semi-empirical systems *and* molecular mechanics (which should work great) fail to reproduce the experimental figures. Or, I've made a mistake. -matt _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Aug 7 18:04:23 1996 Date: Wed, 7 Aug 1996 20:13:11 +0100 (BST) From: A J Turner To: Matthew Harbowy Cc: "hyperchem@hyper.com" Subject: Re: CCL:Branched vs straight chain alkanes Hi! Were the experamental figures gas phase? It seems to me - at a glance - that the AM1 stuff is quite good if you have missed out all the inter molecular terms - including pressure strain in the system etc. Cheers Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Aug 7 18:19:58 1996 Date: Wed, 7 Aug 1996 14:51:28 +22305133 (EDT) From: Michael Kotelyanskii Subject: Re: CCL:Branched vs straight chain alkanes To: Matthew Harbowy Cc: "chemistry@infomeister.osc.edu" , "hyperchem@hyper.com" Just a silly comment: Are you sure, that the energy is calculated in the LOWEST conformation? I mean global, vs. just a local minimum? Michael Kotelyanskii PhD Department of Chemical Engineering University of Delaware kotelyan@che.udel.edu Newark DE 19716 On 7 Aug 1996, Matthew Harbowy wrote: > > In the Handbook of Chem and Physics, it reports > > octane: -49.82 > 2,2,3,3,TMB: -53.99 > > > My results for AM1 and MM+ show (Hyperchem 3.0 calculations) > > am1 mm+ exp > > octane -58.628 (6.448 s.e.) -49.82 > > 2,2,3,3,TMB -40.155 (12.36 s.e.) -53.99 > > ------------- ---------- -------------- ------------ > > oct - tmb -18.473 -5.912 4.17 > > > So, yes, it would seem that both semi-empirical systems *and* > molecular mechanics (which should work great) fail to reproduce the > experimental figures. > > Or, I've made a mistake. > > > -matt > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: Matthew.Harbowy@unilever.com > -- Original Sender From: Address: Matthew.Harbowy@unilever.com > CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator > MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 > Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search > Web: http://ccl.osc.edu/chemistry.html > _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Aug 7 21:52:47 1996 Date: Wed, 7 Aug 96 18:19:14 -0400 From: polowin (Joel Polowin) To: Michael Kotelyanskii , Matthew Harbowy Subject: Re: CCL:Branched vs straight chain alkanes Cc: "hyperchem@hyper.com" , "chemistry@infomeister.osc.edu" > Date: Wed, 7 Aug 1996 14:51:28 +22305133 (EDT) > From: Michael Kotelyanskii > > Are you sure, that the energy is calculated in the LOWEST > conformation? > I mean global, vs. just a local minimum? > > > My results for AM1 and MM+ show (Hyperchem 3.0 calculations) > > > > am1 mm+ exp > > octane -58.628 (6.448 s.e.) -49.82 > > 2,2,3,3,TMB -40.155 (12.36 s.e.) -53.99 I get -58.861 and -40.210 kcal/mol as the heats of formation of the two structures. The former is for the stretched-out conformation of octane, which certainly ought to be the lowest-energy conformation, and the latter is for the symmetrical conformation of 2,2,3,3-tetramethylbutane. A slightly skewed conformation of the latter gives me -41.132 kcal/mol; there might be other still lower-energy conformations. I'm using AM1, lowest state, RHF, converged to an RMS gradient of 0.001 kcal/(A mol). Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 8 03:04:38 1996 From: CreateENBs@aol.com Date: Thu, 8 Aug 1996 00:32:18 -0400 To: BIOTECH@umdd.umd.edu Cc: TOXLIST@cornell.edu, chemecol@iqm.unicamp.br, listserver@ic.ac.uk, napronet@bilkent.edu.tr, aschin-list@nuscc.nus.sg, SAFETY@uvmvm.uvm.edu, ICS-L@umdd.umd.edu, CHEME-L@ulkyvm.louisville.edu, INTERFACE-L@fs4.in.umist.ac.uk, Science_direct@t-online.de, lims@gov.on.ca, CHMINF-L@iubvm.ucs.indiana.edu, MOL-DIVERSITY@listserv.arizona.edu, chemistry@infomeister.osc.edu, isisforum-l@gimli.mdli.com, Analysis-L@fs4.in.umist.ac.uk, hyperchem@hyper.com, methods@net.bio.net, methods@daresbury.ac.uk Subject: DOW CHEMICAL JOINS GLOBAL CONSORTIUM ON ELECTRONIC LAB NOTEBOOKS This is significant news for all scientific laboratory workers who use notebooks and software systems. Please forward this on to interested parties in your organization. We apologize for any duplications that may exist in the mailing lists. ------------------------------------------------------------------------------ ----------- FOR IMMEDIATE RELEASE (8/6/96) Contact: Rich Lysakowski, Ph.D., Executive Director The Collaborative Electronic Lab Notebooks Consortium phone: 508-443-4771 fax: 508-440-9798 (PLEASE DO NOT "REPLY" TO THIS MESSAGE. IF YOU ARE SERIOUSLY INTERESTED IN MORE INFORMATION, THEN PLEASE SEND E-MAIL TO: lysakowski@aol.com ) ------------------------------------------------------------------------------ ----------- DOW CHEMICAL JOINS GLOBAL CONSORTIUM ON ELECTRONIC LAB NOTEBOOKS DOW CHEMICAL HELPS DRIVE COLLABORATIVE ELECTRONIC LAB NOTEBOOKS TO MARKET IN VENDOR-NEUTRAL CONSORTIUM BOSTON, MA--The Dow Chemical Company has joined the Collaborative Electronic Lab Notebooks Consortium. This Consortium of large industrial companies is driving the creation of software systems for electronic lab notebooks and R&D team project data management and collaboration systems for the chemical, pharmaceutical, biotech, food and beverage, oil and gas, and related chemical-based industries. Dow is the fifth Fortune 300 company to join the partnership, along with Air Products and Chemicals and three as yet undisclosed pharmaceutical companies. "Scientists have long needed electronic notebooks as a way to minimize the tedium of lab work. Currently, researchers spend many hours per week writing, transcribing, cutting and pasting and otherwise transferring data in paper notebooks to record their work." observes Dr. Rich Lysakowski, the Consortiums Executive Director. He continues "Yet, paper notebooks are just one part of a much larger system for managing records, data and documents in R&D projects. The paper chase and tedious bottlenecks in productivity must be minimized. In their current paper form, notebooks are very time-consuming to use and costly to manage -- they lock up key information needed to speed up projects." Dr. Lysakowski says further that "Scientists really require very flexible, open and interoperable software tools that integrate electronic lab recordkeeping, project data management, and collaboration processes. This user-driven Consortium is coordinating the efforts of major R&D organizations through an open process that ensures emerging products fit end users needs well." Barbara Sutter, Manager of R&D Proprietary Information and Corporate Information Technology at the Dow Chemical says "The Consortium is a good deal for Dow because from the start we can specify, test and verify that vendors are building what we need -- the result is that our needs get met better, for less money. Our computer users are asking for better tools to enable them to collaborate globally, and be more productive by eliminating redundant and inefficient paper processes." Barb adds "The Consortium has an open software architecture and open business practices that lets us to pick our infrastructure and scientific toolkits ourselves, and integrate them more easily than before. The Consortiums shared vision is consistent with Dows computer strategy. Simply put, it provides us with the best leverage for our money." The two-year Collaborative Electronic Notebooks Consortium is now recruiting additional members, up to a maximum of 15. The Consortium Members are defining and funding the development of commercially-supported electronic notebooks that capture, store and manage electronic records within existing systems for groupware, document management, the World Wide Web, and other systems used in scientific laboratories. The software will permanently record and archive all common types of data from analytical, organic, biochemical, genetic, toxicology and other laboratories, including instrument spectra, chemical structures, documents, spreadsheets, DNA and protein structures, and other data. At the close of the two-year Consortium, full searching and sharing of all common types of notebook information will be possible from the commercially available products. The notebook software clients will be have a modular architecture that include plug-ins that specialize notebooks for different types of labs and job functions. The Consortium is pulling together all necessary pieces, which exist now, and using them in the right combinations to satisfy the major requirements for both scientists and their support staff. For example, the Consortiums lab notebook software systems will allow chemical structures and spectra embedded in existing products to be referenced and easily used, including products such as CAS SciFinder, Beilsteins CrossFire, MDLs ISIS, Daylights tools based on SMILES, Tripos, Oxford Moleculars tools based on CommsManager, Galactic Industries GRAM/3D, Hewlett Packard, Perkin Elmer, Beckman, and many others. Scientists typically use more than one chemical structure handling product and must access specific subsets of the 50+ million compounds in databases spanning several of the aforementioned vendors. Scientists also typically use many different instrument and spectral data systems. Analytical instrument data systems and LIMS are other classes of software that will eventually be integrated into the collaborative electronic notebook systems. The Consortium has already started defining practical standards, benchmarks and best practices for procedures that meet all the major legal and regulatory requirements for open systems that manage electronic records in accurate, trustworthy, reliable ways. The Collaborative Electronic Lab Notebooks Consortium has been operational since December 1995. It expects to deliver its first software and knowledge packages by early 1997. Interested companies with a need for electronic notebooks and team project data management and collaboration systems for R&D and testing labs are invited to join the Consortium now. Consortium Members receive large software discounts, determine system specifications and get early access to software. Potential Members are encouraged to join before October 11, 1996, after which the membership rates will increase. Qualified vendors of electronic lab notebooks, groupware, document and workflow management, LIMS and instrument interfacing systems, scientific information databases, and integration tools will be awarded contracts to develop and support the Consortium software. Companies interested in becoming Consortium Members should contact: Dr. Rich Lysakowski, The Collaborative Electronic Notebooks Consortium, 8 Pheasant Avenue, Sudbury, MA 01776. E-mail: rich@teamscience.com, Tel: 508-443-4771. Fax: 508-440-9798. CONSORTIUM BACKGROUND INFORMATION The electronic lab notebook systems and tools will come from several leading scientific software vendors selected by the Consortium. Because lab data formats and applications are so specialized, varied, and constantly changing, supporting all common scientific lab data types is beyond the scope of any one scientific software vendor. For example, a medium-sized drug company in the consortium states that it must support over 400 different commercial applications every year in Research alone. Application and data integration is an almost insurmountable challenge for end users and support staff. Other key Consortium deliverables include point-and-click application integration tools that encapsulate existing softwares, turning them into standard objects that easily plug into electronic notebooks clients and servers. These tools will allow Consortium Members to configure multivendor solutions at a fraction of current costs. Scientific software markets comprised of niche vendors focused on LIMS, instrument data systems, chemical and biological information systems, and numerous data processing and reporting applications. Niche vendors have failed to meet the legal, regulatory, and systems integration requirements to create successful electronic notebooks -- as evidenced by the failure of the ResearchStation product and Helix Systems, Inc. in 1995 and the withdrawal from the market of the ForeFront Group, Inc.s Virtual Notebook System in 1996. Organic and medicinal chemists working in combinatorial chemistry, high-throughput screening and other types of scientific labs have stated they would like interfaces that give them equal access to each of these products from within the Consortiums electronic notebook systems. The systems must simultaneously serve and go beyond vertical market segments such as chemistry, biology, and materials science. Although chemical structures are important for many research labs, most needs for electronic notebooks exist in labs where few if any chemical structures are used. Companies in the consortium have learned the lesson that they cannot afford to replace their infrastructure with products from scientific niche vendors for something as important as the corporate intellectual property contained in their R&D records. Most R&D companies have already committed their infrastructures to one or more general-purpose base platforms for Web groupware, data, or document handling, such as Lotus Notes, Microsofts Exchange, NetScape WebServers, Documentums EDMS, Interleafs Intellect/BusinessWeb, Saros Mezzanine, Oracle and others. This precludes companies from switching to vertical solutions from a single scientific software vendor. The Consortiums strategy is to leverage existing investments by building on top of and integrating such base platforms, which will be chosen within the next few months. The tools logically must come from several software markets simultaneously. The World Wide Web, MS-Windows, and Macintosh computers are target operating systems for the electronic lab notebook and team project data management systems. _____________________________________________________________________________ The Dow Chemical Company is the largest US chemical company, operating 94 manufacturing sites in 30 countries. Headquartered in Midland, Michigan, USA, Dow is diversified into basic commodity and specialty chemicals, pharmaceuticals, polymers, solvents, agrochemicals, consumer products, and environmental services. Air Products and Chemicals, Inc. is one of the largest suppliers of industrial gases and equipment worldwide. Headquartered in Allentown, Pennsylvania, USA, Air Products maintains a strong partnership with companies in delivering gases for all applications, specialty and intermediate chemicals, and environmental and energy systems. TeamScience, Inc. is the leading international market catalyst firm in scientific software research, engineering, training, consulting and publishing. Headquartered in Sudbury, Massachusetts, USA, TeamScience focuses on consortia and partnerships to deliver scientific applications of groupware, electronic notebooks and records management systems, document management, LIMS, and instrument interfacing systems. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 8 09:30:08 1996 Date: Thu, 08 Aug 1996 12:07:55 +0200 (MET-DST) From: MORGANTINI Pierre-Yves Subject: HyperChem and Windows 95 X-Sender: morganti@sc2a.unige.ch To: hyperchem@hyper.com Hi, We have HyperChem 4.0 (Network version) which run on a Novell server (Netware 3.12) with 10 licenses. The hardware lock is installed on the server and the security server program (NSRVNI.NLM vers. 5.0) is running. We are connected to Novell through the Univesity Network (Ethernet backbone). When we use Hyper- Chem under Windows 3.1 or 3.11, the program obtain a license after 10-20 seconds without problem. Under Windows 95, with Client for Netware Networks and IPX/SPX-compatible protocol installed, we are not able to obtain a license, even after 1 or 2 minutes. Does anybody use about the same configuration and have find a solution? Thank you in advance for your help P.-Y. Morgantini ******************************************************************************* * Pierre-Yves Morgantini * Phone (41-22) 702 65 24 (direct) * * Assistant Professor * (41-22) 702 61 11 * * University of Geneva * * * Department of Physical Chemistry * FAX (41-22) 702 65 18 * * 30, quai Ernest Ansermet * * * 1211 GENEVA 4 (Switzerland) * INTERNET morganti@sc2a.unige.ch * ******************************************************************************* _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 8 14:10:01 1996 From: "Thomas Futterer" To: hyperchem@hyper.com Date: Thu, 8 Aug 1996 14:10:14 +100 Subject: ZINDO/1 calculations Dear Joel Polowin and HyperChem Users, I try to calculate with ZINDO/1the interaction between Ag+ (or alkali cations) and a ligand which contains a double bond and a polyetherchain. What I observe during the optimization is, that the affinity between silver and the olefinic double bond seems to be modeled correctly, but the polyether moves away from silver, which is in contrast to the xray structures. I get similar results trying to calculate the interaction of alkali cations with a polyether. The gradient alternates between 4.00 and 0.30 when I use STEEPEST DESCENT as Algorithm and doesn't decrease anymore. When I use a conjugated gradient method for these calculations the gradient increases ! Does HyperChem has the appropirate tools for modeling interaction of cations (here Ag+, Li+ ---> Cs+) with polyether or am I wrong ? Thank you, Thomas Futterer _________________________________________________ Dipl.-Chem Thomas Futterer Prof.Dr.A.Merz Institut fuer Organische Chemie der Universitaet Regensburg Universitaetsstrasse 31 D-93053 REGENSBURG,Germany Phone: (+) 49 941 943 4650 Fax: (+) 49 941 943 4505 Email: thomas.futterer@chemie.uni-regensburg.de _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 8 15:23:07 1996 Date: Thu, 8 Aug 96 10:48:55 -0400 From: polowin (Joel Polowin) To: patrick kane <94970459@tolka.dcu.ie>, CCL Every , HChem Supp , HChem User Subject: Re: CCL:HyperChem and Schakal > Date: Wed, 7 Aug 1996 13:15:15 +0100 (BST) > From: patrick kane <94970459@tolka.dcu.ie> > > I would be much obliged if anyone tell me if there is a file format > which is compatible with both HyperChem and Schakal. Not according to the information that I can find about Schakal. Schakal is supposed to be able to read a file of atomic names and coordinates; I don't know the exact format that it requires, but you should be able to edit a HIN file down to that by using a text filter such as a small AWK program. A file of atomic symbols and coordinates can be processed into a HIN file by the XRAY2HIN.EXE utility which we have on our ftp/WWW site (ftp://www.hyper.com/pub/other/xray2hin.exe). HyperChem for SGI can read such a file directly. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 8 15:38:26 1996 Date: Thu, 8 Aug 96 11:34:59 -0400 From: polowin (Joel Polowin) To: MORGANTINI Pierre-Yves , hyperchem@hyper.com Subject: Re: HyperChem and Windows 95 > Date: Thu, 08 Aug 1996 12:07:55 +0200 (MET-DST) > From: MORGANTINI Pierre-Yves > > We have HyperChem 4.0 (Network version) which run on a Novell server > (Netware 3.12) with 10 licenses. The hardware lock is installed on the > server and the > security server program (NSRVNI.NLM vers. 5.0) is running. We are connected to > Novell through the Univesity Network (Ethernet backbone). When we use Hyper- > Chem under Windows 3.1 or 3.11, the program obtain a license after 10-20 > seconds without problem. Under Windows 95, with Client for Netware Networks > and IPX/SPX-compatible protocol installed, we are not able to obtain a license, > even after 1 or 2 minutes. Does anybody use about the same configuration and > have find a solution? Can you tell me which network software you are using? We have recently learned from Rainbow that their license server for Novell is incompatible with Microsoft's networking software -- it should be okay with Novell's networking, or with just about anyone's networking *except* Microsoft's. If you are using Microsoft networking, we may be able to help you find a work-around. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 8 19:25:03 1996 Date: Thu, 8 Aug 96 15:54:52 -0400 From: polowin (Joel Polowin) To: Massimo Trotta , hyperchem@hyper.com Subject: Re: Dipol moments II > From: Massimo Trotta > Date: Wed, 7 Aug 1996 12:45:38 +0200 (MET DST) > > > The advantage of ZINDO/1 is that it is parameterized for transition metals. > > For general work on organic compounds, you are probably better off using > > AM1 or PM3. For dipole calculations, AM1 is likely to give slightly > > better accuracy, on average. This may not be true for a particular set > > of molecules which are all rather similar but have some relatively minor > > structural differences. > > I guess the last sentence refers to a general failure of SE methods. Am I > wrong in thinking that methyl groups are not a minor difference? In > particular I am looking to the family of methyl substituted Benzoqinones > (from 1 to 4 substituting methyl groups). Using Zindo I found some > differences among the various dipolar moments. What I mean is that both AM1 and PM3 were optimized for large sets of molecules, using different criteria for what was considered a good fit. For a small set of molecules with similar characteristics, one of the two methods might be consistently better than the other for dipole calculations (and for some other small set of molecules, it might be consistently worse). I do not think it is possible to reliably predict such behaviour. I would tend to think of various methyl-substituted benzoquinones as generally similar since the structures are mostly the same. > > For closed-shell systems you should use RHF; for open-shell systems you > > should use UHF. > > that means that UHF should be applied when the _Next Lowest_ option is > selected. This matches with what I knew, but in the Reference manual of > Vers. 4 (pag. 193) under the voice "spin pairing" is written: > RHF: ................. This method is useful for open- and closed shells. No; it means that UHF is preferable when the multiplicity is greater than 1. The "Next Lowest" state of multiplicity 1 is closed-shell; two electrons have been excited to the same orbital -- for example, both HOMO electrons to the LUMO. You can use RHF calculations for open-shell systems as well as for closed-shell systems, but their accuracy is likely to be poorer than UHF calculations. However, RHF calculations are faster and require less memory than UHF calculations. > Regarding the _Next Lowest_, is it possible to generate a grid for the total > charge density? I tryed to do it via the _Contour Plot_ option, but it > didn't work out. I just ran a single-point AM1 calculation on CH4, specifying a spin multiplicity of 1 and "Next Lowest", then plotted the contour plot for total charge density. No problem. What happened when you tried it -- no contour plot? If so, then my immediate suggestion is that you should check the Z offset in the Grid Control dialogue box. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 8 20:15:22 1996 Date: Thu, 8 Aug 96 17:51:20 -0400 From: polowin (Joel Polowin) To: "Thomas Futterer" , hyperchem@hyper.com Subject: Re: ZINDO/1 calculations > From: "Thomas Futterer" > Date: Thu, 8 Aug 1996 14:10:14 +100 > > I try to calculate with ZINDO/1the interaction between Ag+ (or > alkali cations) and a ligand which contains a double bond and > a polyetherchain. > > What I observe during the optimization is, that the affinity between > silver and the olefinic double bond seems to be modeled correctly, > but the polyether moves away from silver, which is in contrast to the > xray structures. I get similar results trying to calculate the interaction > of alkali cations with a polyether. > > The gradient alternates between 4.00 and 0.30 when I use STEEPEST > DESCENT as Algorithm and doesn't decrease anymore. When I use a > conjugated gradient method for these calculations the gradient increases ! You might get better results by turning off Convergence Acceleration if it is on, or vice versa. This can sometimes affect whether or not the calculation method can converge at all. Convergence can sometimes be a problem for any method, though it seems to happen much more frequently for ZINDO than for other methods. > Does HyperChem has the appropirate tools for modeling interaction of > cations (here Ag+, Li+ ---> Cs+) with polyether or am I wrong ? If you look at the periodic-table charts in the "Setup Menu" chapter of the _Reference_ manual, under "Semi-empirical", you can see which methods have parameters for which elements in the supplied parameter sets. ZINDO/1 is the only method that can handle Ag and the only one for which we supply parameters for K; CNDO, INDO, and ZINDO have parameters for Na, and all methods except PM3 have parameters for Li. When you try to optimize the system using Li or Na, with one of the methods other than ZINDO/1, do you get the same interaction of the cation with the polyether? Remember -- the system you are modelling here is effectively in the gas phase; you must be careful when you compare it to a crystal structure. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 9 08:43:15 1996 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: hyperchem@hyper.com Date: Fri, 9 Aug 1996 11:25:36 +0100 Subject: "Lowest Excited State" in HyperChem Dear HyperChem'ers: On Thu, 8 Aug 96 15:54:52, Joel stated in the message "Dipol moments II" to Massimo Trotta : > The "Next Lowest" state of multiplicity 1 is closed-shell; two > electrons have been excited to the same orbital -- for example, both > HOMO electrons to the LUMO. This is not true! The "next lowest state" does not correspond to the doubly excited HOMO-LUMO configuration, and it is not closed-shell. In HyperChem, the next lowest singlet state S(1) of a molecule with closed-shell ground state S(0) is assumed to correspond to the singly excited HOMO-LUMO configuration, i.e. the configuration where ONE electron has been promoted from HOMO to LUMO. This is an open-shell configuration, and one singlet state S(1) and the three degenerate components of a triplet state T(0) may be projected from it. Generally, T(0) has lower energy than S(1), as predicted by "Hund's rule". HyperChem applies a spin-averaged pseudo-closed-shell approximation in the RHF treatment of S(1), using a representation equivalent to Dewar's "half-electron" method. In this approximation, singlet and triplet spin states are scrambled during the SCF procedure. This means that MO wavefunctions and MO energies are identical for S(1) and T(0), provided the nuclear coordinates are identical. The total energies projected for S(1) and T(0) are of course different, but the gradients are the same! Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757711 Roskilde University (RUC) Fax: +45 46757721 POB 260, DK-4000 Roskilde, Denmark E-Mail: JSL@virgil.ruc.dk =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 9 14:53:45 1996 Date: Fri, 9 Aug 96 10:47:56 -0400 From: polowin (Joel Polowin) To: "Jens Spanget-Larsen" , hyperchem@hyper.com Subject: Re: "Lowest Excited State" in HyperChem > From: "Jens Spanget-Larsen" > Date: Fri, 9 Aug 1996 11:25:36 +0100 > > > The "Next Lowest" state of multiplicity 1 is closed-shell; two > > electrons have been excited to the same orbital -- for example, both > > HOMO electrons to the LUMO. > > This is not true! The "next lowest state" does not correspond to the > doubly excited HOMO-LUMO configuration, and it is not closed-shell. > In HyperChem, the next lowest singlet state S(1) of a molecule with > closed-shell ground state S(0) is assumed to correspond to the singly > excited HOMO-LUMO configuration, i.e. the configuration where ONE > electron has been promoted from HOMO to LUMO. This is an open-shell > configuration, and one singlet state S(1) and the three degenerate > components of a triplet state T(0) may be projected from it. > Generally, T(0) has lower energy than S(1), as predicted by "Hund's > rule". [etc.] Oops. You're right. I checked with our semi-empirical expert; it seems that I understand these calculations less well than I had thought. Thank you for the correction. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 9 19:06:53 1996 Date: Fri, 9 Aug 96 16:43:26 -0400 From: polowin (Joel Polowin) To: Paul Scott , hyperchem@hyper.com Subject: Re: Hydration energy calculations Update on the hydration energy calculations: no, selecting only part of the system doesn't seem to help; it appears that QSAR Properties is still trying to get the entire structure before it does the calculation on only part of it, and I am still getting the "Error in DoCalculation" message. It is obviously a bug/limitation (I have added it to the bug list), and I am not sure if there is a work-around. If I find one, I will post it on the list. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 9 19:22:59 1996 Date: Fri, 9 Aug 96 16:29:46 -0400 From: polowin (Joel Polowin) To: Paul Scott , hyperchem@hyper.com Subject: Re: Hydration energy calculations > Date: Tue, 23 Jul 1996 22:55:06 -0600 (MDT) > From: Paul Scott > > I want to do some approximate calculations on changes in hydration > energy on oligomerization of small protein subunits and seem to have run into > a bug (or memory limitation?) in the hydration energy module of ChemPlus > 1.5 (ruuning with HyperChem 4.0 on a Pentium 133 with 16 MB RAM). Once the > size of the protein reaches around 2100 atoms the > calculation crashes with the enigmatic and unhelpful message "Error in > DoCalculation". Surprisingly calculations of other additive Qsar > properties such as LogP, surface area (grid) and volume keep going but > surface area (approximate) crashes at the same time as the hydration > energy calculation. Is there a fix or a work-around for this problem? While trying to track this down, I have found several problems with the hydration energy calculation. First: this calculation is based on the "surface area (approximate)" calculation, so it is not too surprising that they would fail under the same circumstances. One of the limitations of the surface area calculation is that it tends to be unreliable for calculating more than one molecule at once; it warns the user of this. When multiple molecules are used and they are close together, the results degrade from fair to poor to just plain silly. The hydration energy calculation does *not* warn users of this potential problem, even though it is subject to the same effect (though it seems to be less affected than the surface area calculation). I have added this to the bug list. Next: the size problem. If the structure is too large -- say, 2100 atoms -- my machine starts to thrash and grind its hard drive a few minutes after I start the calculation. If the structure is a bit smaller (1964 atoms in one specific case) and I have several other programs running, I get a "DDE Error: Out of memory" message. If I close down the other programs and reduce the structure a bit more, I get the "Error in DoCalculation: No Resume" error. This is a general message that means that *something* has gone wrong with the program that the programmer didn't set up a specific process to handle. It appears to be a buffer size problem, though I am not yet certain of this. It *should* be possible to work around the problem by selecting only part of the system in the workspace for calculation, then selecting another part, etc., such that the parts sum to the whole. This works, and gives correct results, for small systems. I will try to test this for large systems over the next few days. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Sat Aug 10 13:44:51 1996 From: ps@ocisgi7.unizh.ch (Serge Pachkovsky) Subject: Re: "Lowest Excited State" in HyperChem To: jsl@virgil.ruc.dk (Jens Spanget-Larsen) Date: Sat, 10 Aug 1996 17:44:57 +0200 (MDT) Cc: hyperchem@hyper.com Hi, > triplet spin states are scrambled during the SCF procedure. This > means that MO wavefunctions and MO energies are identical for S(1) > and T(0), provided the nuclear coordinates are identical. The total > energies projected for S(1) and T(0) are of course different, but the > gradients are the same! The statement above concerning gradients of the energy in the first excited singlet and the lowest triplet state in the half electron method is, strictly speaking, wrong. Equivalence of the gradients would imply that all smooth patches of the singlet and triplet potential energy surfaces should differ *by*a*constant*. By looking at the corresponding energy expressions, one can easily see that the difference is actually twice the magnitude of the exchange integral between two partially occupied MOs in the half-electron method, which is most certainly not a constant. However, the statement above is right in the practical sense: Since Hyperchem implements only approximate gradients of the energy in the half-electron method, (wrong) gradients of the energy computed by Hyperchem will in fact be identical for the two states. In my experience, the difference between approximate and correct gradients is typically of the order of 1-10 kcal/mol/A for "normal" organic systems, but may be *much* larger for extensive conjugated systems or in the vicinity of the singlet-triplet crossing. Regards, /Serge.P _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Aug 12 08:40:57 1996 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: ps@ocisgi7.unizh.ch (Serge Pachkovsky), hyperchem@hyper.com Date: Mon, 12 Aug 1996 10:59:16 +0100 Subject: Re: "Lowest Excited State" in HyperChem Serge sent: > > triplet spin states are scrambled during the SCF procedure. This > > means that MO wavefunctions and MO energies are identical for S(1) > > and T(0), provided the nuclear coordinates are identical. The total > > energies projected for S(1) and T(0) are of course different, but the > > gradients are the same! > > The statement above concerning gradients of the energy in the first excited > singlet and the lowest triplet state in the half electron method is, strictly > speaking, wrong. Equivalence of the gradients would imply that all smooth > patches of the singlet and triplet potential energy surfaces should differ > *by*a*constant*. By looking at the corresponding energy expressions, one > can easily see that the difference is actually twice the magnitude of the > exchange integral between two partially occupied MOs in the half-electron > method, which is most certainly not a constant. > > However, the statement above is right in the practical sense: Since Hyperchem > implements only approximate gradients of the energy in the half-electron > method, (wrong) gradients of the energy computed by Hyperchem will in fact > be identical for the two states. In my experience, the difference between > approximate and correct gradients is typically of the order of 1-10 kcal/mol/A > for "normal" organic systems, but may be *much* larger for extensive conjugated > systems or in the vicinity of the singlet-triplet crossing. > > Regards, > > /Serge.P > Thank you very much for your remarks! My "insight" into the gradient question was limited to the observation that HyperChem actually do predict identical gradients for S(1) and T(0). Yours sincerely, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757711 Roskilde University (RUC) Fax: +45 46757721 POB 260, DK-4000 Roskilde, Denmark E-Mail: JSL@virgil.ruc.dk =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Aug 12 10:40:23 1996 Date: Mon, 12 Aug 96 02:54:29 CST From: "Irina K. Vorontsova" Reply-To: To: hyperchem@hyper.com Subject: Working with Z-matrix Dear neters, how can one start 'hyperchem' using Z-matrix? Thanks for help, Irina Vorontsova _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Aug 14 20:58:36 1996 From: "Scott Morgan" Organization: Dana College To: hyperchem@hyper.com Date: Wed, 14 Aug 1996 16:47:48 CDT Subject: calculating transition state structures. Hi! I'm a relatively new user of Hyperchem and am interested in calculating transition state structures. This question may be rather broad, but, how does one go about approaching this problem? I have minimized structures for the starting material and final product (they happen to be a carbene and an alkene) -- where do I go from here? Thanks in advance for any suggestions. You can reply to me directly if you wish. SCM Dr. Scott C. Morgan Assistant Professor of Chemistry Dana College Blair, NE 68008 (402)426-7263 smorgan@acad2.dana.edu _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Aug 14 22:51:56 1996 Date: Wed, 14 Aug 96 20:48:17 -0400 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: HyperChem mailing list In response to the incredible wave of "unsubscribe" messages that has recently washed over the list, I would like to remind our list users that such messages should be sent to "hyperchem-request@hyper.com" -- the automatic administrative address -- and, emphatically, NOT to the list itself. Subscription requests should, of course, also be sent to the same address. If you require human intervention, please send messages to "listadmin@hyper.com", or to "support@hyper.com". Thank you. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 15 15:17:19 1996 Date: Thu, 15 Aug 96 12:04:10 -0400 From: polowin (Joel Polowin) To: hyperchem@hyper.com, Subject: Re: Working with Z-matrix > Date: Mon, 12 Aug 96 02:54:29 CST > From: "Irina K. Vorontsova" > > how can one start 'hyperchem' using Z-matrix? If you start HyperChem from the File/Run menu item in the File Manager or Program Manager, or otherwise start it with a text command instead of just clicking on the icon, you can specify a file name as a command line argument. If that file has the extension ".HIN" or ".ENT", HyperChem will start by opening that file in the HIN or PDB format, respectively. HyperChem will not automatically start by opening a file in any other format. Depending on what you need to do, you might be able to create a script file which tells HyperChem to switch to the Z-matrix format for files, and then reads the file. If that script file is named CHEM.SCR and is in the HyperChem directory, it will be executed automatically when HyperChem starts, which will then make HyperChem open that Z-matrix file. Or if you specify the script file name (with the extention ".SCR") as a command line argument as above, HyperChem will run the script when it starts. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Mon Aug 19 18:08:51 1996 Date: Mon, 19 Aug 96 14:46:01 -0400 From: polowin (Joel Polowin) To: "Scott Morgan" , hyperchem@hyper.com Subject: Re: calculating transition state structures. > From: "Scott Morgan" > Date: Wed, 14 Aug 1996 16:47:48 CDT > > I'm a relatively new user of Hyperchem and am interested in > calculating transition state structures. This question may be rather > broad, but, how does one go about approaching this problem? I have > minimized structures for the starting material and final product > (they happen to be a carbene and an alkene) -- where do I go from > here? Our current optimizers do not do transition-state searching; they look only for minima, not saddle points. It *is* possible to do a sort of transition- state searching by using external control by other software, or even a script file. In this case, some set of structural parameters are restrained to fixed values -- a pair of bond distances between two fragments and one atom, for example -- and optimizations performed between regular variations in the restrained values. The next release of HyperChem will include some form of transition-state searching. I do not have any details about the function yet; the formal product announcement will be made at the ACS meeting in Orlando next week. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Wed Aug 21 07:55:25 1996 From: "Gregor Fels" Organization: Universitaet-GH Paderborn FB13 To: hyperchem@hyper.com Date: Wed, 21 Aug 1996 10:58:21 GST Subject: HyperChem User Meeting in Germany HyperChem User Meeting in Germany I had the pleasure to host the first European HyperChem course organized by HyperCube early this year and to take part in the teaching. At least from my narrow point of view, we had three productive and pleasing days of hard working that were very satisfying. To me, the course gained much from the broad spectrum of participants, interests, questions, and skills, of course next to the fact that it was run by Dragan Vuckovic, the outstanding expert from HyperCube. Encouraged by this, I am thinking of a more regular get together of HyperChem users in Germany (or Europe) to share science and teaching stuff, news and views, scripts and macros, and whatever you would like to through in. This should be done in an informal environment and perhaps could take place at the university of Paderborn where we would supply the necessary facilities including enough computers to demonstrate things and to have hands on the program (PC- and SGI-version). If there is time and interest we even might want to set up a short program that looks over the rim and e.g. demonstrates non HyperCube software that cooperates with HyperChem. I would appreciate to receive your comments on this idea to decide whether it is worth planing such a meeting and spending the necessary effort to organize it. Answers is English or German are equally welcome. Things to consider would be for instance: - what would you expect of such a meeting - how much time would you feel is adequate for it - would you like to actively contribute with a problem, question, result, application, demonstration, macro, script etc. covering any area of scientific or educational use or aspect of the program - would you also come if you cannot (or don't want) to contribute - would Paderborn be located convenient enough for you to participate - which time of the year would suit you best. Please pass on this message to colleagues who are HyperChem users but who presumably will not be reached by this mail. Looking forward to your answers Gregor Fels Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 0049-5251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 23 10:09:35 1996 Date: Fri, 23 Aug 1996 10:09:28 -0700 From: Alasdair Elliot Organization: Natal Technikon To: HYPERCHEM@HYPER.COM Subject: HYPERCUBE I AM LOOKING AT USING HYPERCHEM AS A RESEARCH TOOL TO PRODUCE 3-D MODELS OF SYNTHETIC ORGANIC DYESTUFFS. HAS ANYONE EXPERIENCE IN THIS FIELD _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 23 16:00:18 1996 Date: Fri, 23 Aug 1996 18:05:51 +0100 (BST) From: patrick kane <94970459@tolka.dcu.ie> To: CCL Every , HChem User , HChem Supp Subject: Geometry Optimisations with Scripts in HyperChem Hi, I am a HyperChem user. When I wish to run molecular mechanics geometry optimisations (using MM+) with scripts I find that the termination conditions (the RMS gradient and the max number of cycles) and the screen refresh period do not change when the script is run. Instead, I need to carry out a 'manual' geometry optimization on some molecule (not necesarily one of those molecules referred to in the script) with the required settings, stop the optimisation after a few seconds and then run the script. This is very tedious and I would be very grateful if anyone could provide a solution. If it helps, the offending script commands are typically: optim-max-cycles 4000 optim-convergence 0.01 optim-algorithm newtonraphson (THIS LINE DOES NOT CAUSE ME A PROBLEM) screen-refresh-period 200 Regards, Paddy. Paddy Kane School of Chemical Sciences Dublin City University Ireland 94970459@tolka.dcu.ie --------------------------------------------- --------------------------------------------- _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 23 18:46:02 1996 Date: Fri, 23 Aug 96 17:19:24 -0400 From: polowin (Joel Polowin) To: patrick kane <94970459@tolka.dcu.ie>, HChem Supp , HChem User , CCL Every Subject: Re: CCL:Geometry Optimisations with Scripts in HyperChem > Date: Fri, 23 Aug 1996 18:05:51 +0100 (BST) > From: patrick kane <94970459@tolka.dcu.ie> > > I am a HyperChem user. When I wish to run molecular mechanics geometry > optimisations (using MM+) with scripts I find that the termination > conditions (the RMS gradient and the max number of cycles) and the screen > refresh period do not change when the script is run. Instead, I need to > carry out a 'manual' geometry optimization on some molecule (not > necesarily one of those molecules referred to in the script) with the > required settings, stop the optimisation after a few seconds and then run > the script. This is very tedious and I would be very grateful if anyone > could provide a solution. > > optim-max-cycles 4000 > optim-convergence 0.01 > optim-algorithm newtonraphson (THIS LINE DOES NOT CAUSE ME A PROBLEM) > screen-refresh-period 200 The maximum number of cycles *can* be set with the script command. However, when you open the Geometry Optimization dialogue box, it automatically resets the number of cycles to the default value, which is 15 times the number of atoms. If you run the optimization with the "do-optimization" script command, the optimization will run to the number of cycles that you specify with "optim-max-cycles". I find that the "optim-convergence" script command behaves as it should, and it correctly sets the value in the dialogue box as well. Several of the script commands for the screen refresh period for dynamics and optimization seem to have gotten mixed up; this is in the bug list. The "screen-refresh-period" script command changes the refresh period for molecular dynamics but not for geometry optimization. Currently, "dynamics-collection-period" changes the collection period for dynamics and the screen refresh period for optimization. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. _______________________________________________________________________________ From owner-hyperchem@hyper.com Thu Aug 29 17:41:12 1996 Date: Thu, 29 Aug 1996 11:57:32 -0700 (PDT) From: Scott Kellogg X-Sender: skellogg@harrier.csrv.uidaho.edu To: Hyperchem Subject: Re: Computational Chemistry > Are there computer programs that can calculate fluorescence, or perhaps > excitation/emission wavelengths? We are working with some new > fluorophores and determining their structures and I was just > wondering about computational chemistry approaches to fluoresence. > If anyone should know it would be Molecular Probes. Thanks. > > =================================================================== > Scott T. Kellogg, Dept. of Microbiol., Mol. Biol. & Biochem. > Univ. of Idaho, Moscow, ID 83844-3052 Internet: skellogg@uidaho.edu > Phone: 208-885-6966 Fax: 208-885-6518 _______________________________________________________________________________ From owner-hyperchem@hyper.com Fri Aug 30 13:57:28 1996 Date: Fri, 30 Aug 1996 10:33:09 -0400 (EDT) From: "Steven A. Clarke" X-Sender: clarkes@pacman.rs.itd.umich.edu To: hyperchem@hyper.com Subject: HyperChem 4.0 and Novell VLM 1.20 (941108) Hello All We recently upgraded computers and networks, and now have an appearent conflict between the network VLM driver and the security lock on HyperChem. Is anyone out there using VLMs from Novell successfully with HyperChem, and if so, which versions? Did you have to set up anything in a special way, etc? thanks for your help Steve Clarke ****************************************************************** * Steven Clarke * Dept of Chem Univ of Mich * clarkes@umich.edu * ****************************************************************** * You are Finite, Zathras is Finite, this is . . . Wrong Tool! * * Zathras, WWEII, Babylon 5 * ****************************************************************** * We have been looking for home and keep finding this sandpit. * * Maybe if start looking for this sandpit, we will find our home!* * Winnie the Pooh * ******************************************************************