From owner-hyperchem@hyper.com Tue Jan 2 19:11:21 1996 Date: Tue, 2 Jan 96 15:44:32 -0500 From: polowin (Joel Polowin) To: Daniel Kost Subject: HyperChem: shallow potentials Cc: hyperchem@hyper.com > Date: Tue, 26 Dec 1995 08:42:01 +0200 (IST) > From: Daniel Kost > > I use Hyperchem to calculate molecular donor-acceptor (CT-charge > transfer) complexes. Typically Hyperchem will optimize the various > geometrical parameters (using AM1 or PM3), but will fail miserably on > shallow potentials, such as the distance between the two aromatic rings > belonging to acceptor and donor. Depending on the initial distance, > Hyperchem reports different final distances (for example, if we start > with 4.5 A for the distance between parallel benzene rings, it converges > to something like 4.55, and if we use 5.0 A for the initial value we end > up with something like 4.9. for the very same pair of donor and acceptor > molecules). We tried to tighten the convergence, but this did not solve > the problem. > What finally did solve the problem, was running the optimization using > GAUSSIAN94 software, with the same AM1 and PM3 levels. The optimization > converged to the same value from both sides. Our semi-empirical algorithms are the standard literature ones, and the results of a semi-empirical calculation with HyperChem have not yet been found to differ from the results of the same calculation performed with other software. Our software and Gaussian's use different optimization algorithms, so different paths might be followed down the potential surface, but in either case you should end up in the same place. To optimise a structure with a shallow potential, you should use small values for both the optimization termination condition and the SCF convergence limit (and a sufficiently large value for the maximum number of cycles). You should make sure that the electronic state is the one that you actually want, for example by looking at the charge distribution and/or the contour plots. It is also possible that HyperChem is finding and settling into local minima near the starting points, while Gaussian is finding a single deeper minimum between them. I do not know of any general method for avoiding this problem, other than a bit of molecular dynamics work, or otherwise disturbing the system a bit so that HyperChem doesn't immediately find the local minimum. If the entire system is shifting slightly, the optimiser is less likely to be caught in a shallow local minimum. Regards, 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 Jan 3 14:21:19 1996 Date: Wed, 3 Jan 96 09:59:27 -0500 From: polowin (Joel Polowin) To: Daniel Kost Subject: Re: HyperChem: shallow potentials Cc: hyperchem@hyper.com > From polowin Tue Jan 2 15:44:32 1996 > > Our semi-empirical algorithms are the standard literature ones, and the > results of a semi-empirical calculation with HyperChem have not yet been > found to differ from the results of the same calculation performed with > other software. Our software and Gaussian's use different optimization > algorithms, so different paths might be followed down the potential > surface, but in either case you should end up in the same place. I should also note that the three different optimization algorithms that are available in HyperChem would follow different paths down the potential surface. If your problem is indeed the result of HyperChem finding local minima near the starting points, then using the Steepest Descent method might let you find other minima since it would tend to wander around the potential surface more than the other methods do. 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 Jan 3 21:12:50 1996 From: Gerardo Burton To: "'hyperchem@hyper.com'" Subject: Hyperchem minimizers Date: Wed, 3 Jan 1996 19:31:52 -0300 Hi just to add some of our observations with respect to the optimization = algorithms implemented in Hyperchem. It is true that these are the = standard literature ones, but it should be noted that they are not the = best nor the most commonly used with semiempirical methods. MOPAC and = its commercial version AMPAC use as default the BFGS = (Broyden-Fletcher-Goldfarb-Shano) algorithm which far more efficient = than those implemented in Hyperchem. We currently use AMPAC 5.0 in a Sun = workstation and Hyperchem in a Pentium 90 and besides the obviously = different computing speeds, we could verify that BFGS will find the = minimun in less iteration cycles than Hyperchem using Polak-Ribiere or = Fletcher-Reeves (we could never find a difference between this two). = This is specially true in shallow potential minima, where the number of = cycles needed by AMPAC may be over an order of magnitude smaller keeping = the sameconvergence criteria! This would imply at least ten times faster = calculations at comparable computing speed and of course is the reason = why Gaussian also uses this type of algorithm for Ab-initio = calculations. We have also found some shallow potential minima in which Hyperchem is = unable to converge (at least in reasonable times), for example when = acetates are involved in certain structures like steroids. One can = easily see, following the minimization, that the structure oscillates = slowly back and forth around the minimun (rotation around C-O-C bonds). = The same structure optimized with BFGS in AMPAC will converge almost = immediately without noticeable oscillations. An implementation of BFGS into Hyperchem would be interesting. Also = implementation of a quadratic algorithm (Newton) for the semiempirical = methods would be helpful for refining structures and/or avoiding saddle = points in difficult structures. Is there a chance we may see some of = these in future releases? Regards Gerardo Gerardo Burton e-mail: burton@quimor.qo.fcen.uba.ar Departamento de Quimica Organica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Tel/FAX 54 1 788-6915 ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jan 4 14:51:58 1996 Date: Thu, 4 Jan 96 10:49:04 -0500 From: polowin (Joel Polowin) To: Gerardo Burton , "'hyperchem@hyper.com'" Subject: Re: Hyperchem minimizers > From: Gerardo Burton > Date: Wed, 3 Jan 1996 19:31:52 -0300 > An implementation of BFGS into Hyperchem would be interesting. Also > implementation of a quadratic algorithm (Newton) for the semiempirical > methods would be helpful for refining structures and/or avoiding saddle > points in difficult structures. Is there a chance we may see some of > these in future releases? Improvement of our optimization algorithms is a high priority for development for future releases. It is pretty certain that the next release of HyperChem will have some significant improvements in this area. But the details have not been determined absolutely; this is work in progress. 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 Jan 4 15:00:24 1996 From: Journal of Molecular Modeling Subject: Journal of Molecular Modeling 1996 To: hyperchem@www Date: Thu, 4 Jan 1996 16:22:00 +0100 (MET) Journal of Molecular Modeling the advanced way of publishing We would like to thank all those who helped us through the startup phase of this exciting project for their cooperation. A special thanks goes to our authors for choosing the Journal of Molecular Modeling as their publication platform of choice for presenting their latest results, showing confidence in the promising project of electronic publishing. We hope you'll continue to help us shape the future of scientific publishing in a multimedia world. Wishing that the new year proves to be creative and prosperous, we are looking forward to welcome you as an author of the Journal of Molecular Modeling. If you haven't already subscribed to the journal, please consider placing a personal subscription (at a very favour- able price) or discuss an institutional susbcription with colleagues and your librarian. Detailed information on the online journal, its Annual CD-ROM and Print Archive Edition, is available via WWW at the URL given below. With professional best wishes for 1996. Tim Clark Henryette Roth (editor) (assistant editor) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ Journal of Molecular Modeling ^ Tel: [+49](0)9131 / 85-2948 ^ ^ Computer-Chemie-Centrum ^ [+49](0)9131 / 85-6567 ^ ^ Universitaet Erlangen-Nuernberg ^ ^ ^ Naegelsbachstrasse 25 ^ Fax: [+49](0)9131 / 85-6565 ^ ^ D-91052 Erlangen ^ ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ email: jmolmod@organik.uni-erlangen.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ URL: http://www.organik.uni-erlangen.de/info/JMOLMOD/jmolinfo.html ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jan 10 15:53:22 1996 Date: Wed, 10 Jan 1996 14:14:35 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: Chiral Selectivity To: hyperchem@hyper.com, support@hyper.com Cc: chemistry@infomeister.osc.edu Hi, Happy New Year. I am a HyperChem user and I wish to study the chiral selectivity of some molecules. I wish to study why some chiral substrates of a given configuration are more selective towards eithier the R- or S- forms of for example, phenylethylamine. Firstly, can anyone point me to some general references on this subject. Secondly, Can anyone advise me on the best way to model such interactions with HyperChem. More specifically, I would like to know: a) how I should initially place the phenylethylamine molecule. Presumably, I should place the chiral region of the phenylethylamine molecule near the chiral region of the substrate but can anyone be more specific than this. b) should I model such interactions with bond dipoles or atomic charges Kind regards, Paddy Paddy Kane 94970459@vax1.dcu.ie ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jan 11 06:44:44 1996 Date: Thu, 11 Jan 1996 17:29:17 +1000 From: Tony Hughes Subject: automating RMS overlays To: hyperchem users group Subject: Time: 5:13 PM OFFICE MEMO automating RMS overlays Date: 1/11/96 Dear HyperChem users, I'd like to know if its possible to use Excel/Visual Basic to drive the RMS overlay module of Chemplus from HyperChem to automate a series of RMS overlays of different atom sequences from a given pair of molecules. Simply treating "RMS overlay" as a normal HyperChem menu item in a visual basic module does not work. Do the individual ChemPlus modules themselves support DDE? Thanks in advance for any head scratching! Tony Hughes ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jan 11 15:10:44 1996 Date: Thu, 11 Jan 96 09:47:14 -0500 From: polowin (Joel Polowin) To: Tony Hughes , hyperchem users group Subject: Re: automating RMS overlays > Date: Thu, 11 Jan 1996 17:29:17 +1000 > From: Tony Hughes > > I'd like to know if its possible to use Excel/Visual Basic to drive the RMS > overlay module of Chemplus from HyperChem to automate a series of RMS overlays > of different atom sequences from a given pair of molecules. Simply treating > "RMS overlay" as a normal HyperChem menu item in a visual basic module does > not work. Do the individual ChemPlus modules themselves support DDE? The only ChemPlus module that supports DDE links from outside is the QSAR Properties module, so I don't think that you can use Excel or Visual Basic to run RMS Overlay. You would have to have the external control at a higher level, such as the Windows macro recorder. I don't know if that recorder is flexible enough for this kind of work, but I think it isn't. 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 Jan 12 19:47:36 1996 From: /G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com Date: Fri, 12 Jan 1996 13:32:00 -0500 To: hyperchem@hyper.com Cc: chemistry@infomeister.osc.edu Subject: Re: CCL:Chiral Selectivity -Reply >Date: Fri, 12 Jan 1996 11:25:22 +0100 >One of the problems to be aware of is that in real life there will not >be 100 % enantioselectivity. Hence there are probably two pathways to >product, one going through a higher energy pathway than the other, >which corresponds to the chiral selectivity observed. This real energy >difference only has to be small to give large enantiomeric excesses. >Unfortunately, I feel the accuracy of the calculations involved can be >less than the accuracy required. The good minimisers available today >would prefer to seek out this global minimum - corresponding to the ^^^^^^^^^^^^^^ >product in excess, and hide the pathway that gives the other >enantiomer - hence hiding valuable information. The vast majority of minimization algorithms *do not* see global minima, but the *nearest* minimum. While small differences in energy do represent large differences in enantioselectivity, this says nothing about the potential energy surface and two 'minima' can have drastically different geometies and can be separated by fairly large energy barriers, allowing good discernment between minima. In addition, it should be noted that enantioselective catalysts may result in different geometries/energies for the transition state of one isomer or the other, so doing an 'optimization' of a 'minimum' is not always the desired calculation. True differences in product distributions should only be measurable by dynamic modeling of an ensemble of conformations. One should be able to minimize to both enantiomers (which should be exactly the same energy in vacuo/in the absence of other molecules). One should be able to minimize a catalyst. But the tacking of substrate onto catalyst requires good intermolecular paramaters, and a simple 'minimization' will probably see hunderds of local minima, depending on orientation. It is less that you hide the unfafored enantiomer, but that you have no idea whether you're at the 'true' preferred conformers for either favored *or* unfavored. In short, such modelling is clearly beyond the limited capabilities of Hyperchem at the present time. >My advice is therefore to try and explain things in terms of steric >hindrance to explain the observed chiral selectivity, and apply a little >chemical intuition before trusting the numbers generated. Try to think of >how the enantiodifferentiation could occur, and place the reactant in a >relavant orientation wrt to the chiral adduct and then perform a >minimisation. Do this for both enantiomers. Not an ideal situation I know >but it may help. At that point, you have to ask, why are you doing computer modeling? If you are using a massively qualitative model, why go through the expense of extended computation if you can make good 'guesses' with chemical intuition? At some point, it seems that one is using 'modeling' to generate good 'visualizations' and not much 'data'. That seems like a fine use of hyperchem, to easily generate 3-d models for visualization, but it would seem that any computation one does will be heavily biased by the model. All assumptions should be designed to be falsifiable: that is, you can say the opposite, and prove it is untrue. Additionally, what parameters do you use? Molecular Mechanics? At some point, you'll need to create a new parameter specific to your model, one which you can 'fudge' but have a good justification for doing so. Then minimizations can occur; but with 'standard' parameters, I'm not sure how well intermolecular and electronic effects are reproduced. matt ________________________________________________________________________ From simonk@matthey.com Fri Jan 12 20:12:55 1996 From: simonk@matthey.com Date: Fri, 12 Jan 1996 11:26:05 -0500 >Date: Fri, 12 Jan 1996 11:25:22 +0100 To: hyperchem@hyper.com, support@hyper.com, 94970459@vax1.dcu.ie Cc: chemistry@infomeister.osc.edu Subject: Chiral Selectivity -Reply With regards to Paddy Kanes enquiry concerning chiral selectivity. I performed a little work in this area using HyperChem to look at Enantioselective hydrogenation of methyl pyruvate cataysed by cinchona alkaloid modified Pt catalysts. The problem being that calculations are not really possible in this system, hence I ended up performing integrations by eye. The results were however satisfactory. Simons et al Rec. Trav. Chim Pay-Bas 1994 113 465 cf Schwalm et al Catal Lett 23 1994 271 One of the problems to be aware of is that in real life there will not be 100 % enantioselectivity. Hence there are probably two pathways to product, one going through a higher energy pathway than the other, which corresponds to the chiral selectivity observed. This real energy difference only has to be small to give large enantiomeric excesses. Unfortunately, I feel the accuracy of the calculations involved can be less than the accuracy required. The good minimisers available today would prefer to seek out this global minimum - corresponding to the product in excess, and hide the pathway that gives the other enantiomer - hence hiding valuable information. My advice is therefore to try and explain things in terms of steric hindrance to explain the observed chiral selectivity, and apply a little chemical intuition before trusting the numbers generated. Try to think of how the enantiodifferentiation could occur, and place the reactant in a relavant orientation wrt to the chiral adduct and then perform a minimisation. Do this for both enantiomers. Not an ideal situation I know but it may help. Cheers, Keith ********************************************************************* Dr. Keith Simons TEL: +44-(0)1763-253126 Senior Development Chemist FAX: +44-(0)1763-253516 Johnson Matthey E-Mail simonk@matthey.com Process & ElectroCatalyst Development Orchard Road Royston Herts. SG8 5HE UK ********************************************************************** ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jan 16 16:55:33 1996 Date: Tue, 16 Jan 96 11:52:14 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: SN1 reactions I have had occasional requests for simulations of SN1 reactions with HyperChem, but I have had a lot of trouble in getting one to work. I finally figured out what was going wrong, and I managed to run an SN1 reaction. I have appended the HIN file below. Something like a thermal dissociation is easy: just select each part of the system, and use Set Velocity to get them moving in opposite directions. Molecular dynamics with a semi-empirical method will give the dissociation. The problem comes when one wishes to bring two fragments together and get them to stick together: the energy of collision tends to be converted to potential energy, and then back, making the fragments separate again. In real life, the system might lose this energy by radiation (which we can't model) or by transfer to other vibrational modes in the structure (difficult in the simple structures that we use for these demonstration simulations), or by interaction with other molecules. The trick that I discovered is to run the simulation once to find out the collision time, the time at which the two fragments are at a reasonable bond distance and beginning to move apart rapidly. Then the simulation is repeated, with 'Run Time' set to that collision time, and 'Cool Time' used for the remaining time. When the dynamics run switches from 'Run Time' to 'Cool Time', all of the velocities of atoms in the system are rescaled to a distribution of values appropriate for that temperature. This instantly gets rid of most of the kinetic energy of the two fragments, and one is left with a bonded structure with some vibrational excitation. The reaction that I have modelled is a two-step SN1: (1) IC(CH3)3 --> C(CH3)+ + I- (thermal, slow, rate-determining) (2) C(CH3)3+ + Cl- --> ClC(CH3)3 (fast) If the cooling step is not used, the Cl- tends to bounce off the tertiary C atom (and the semi-empirical calculation tends to blow up as the Cl atom moves away). For slightly different starting positions of the Cl-, it abstracts a proton instead of sticking, leading to HCl + (CH3)2C=CH2 . The settings and options for the dynamics calculation are described in the comments at the beginning of the .HIN file. 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. ; SN1.HIN ; Models the SN1 reaction tBuI --> tBu+ + I- (slow, rate-determining) ; tBu+ + Cl- --> tBuCl (fast) ; Settings: ; Semi-empirical; AM1; total charge -1; spin multiplicity 1 ; SCF convergence limit 0.01; 50 iterations; convergence acceleration on ; lowest state; RHF; no CI ; Molecular dynamics: Heat time 0; Run time 0.21 ps; Cool time 0.21 ps ; Time steps 0.001 ps; Start T = 0 (greyed out); Simulation T = 300; ; Final T = 299; T step = 1 ; In vacuo; not constant T; Data collection 1 step; Screen refresh 1 step ; Restart on. ; Joel Polowin, Hypercube Inc., Jan. 16 1996 forcefield mm+ sys 250.3708 view 40 0.12848 55 15 0.9962287 0.04796445 -0.07230323 -0.05712888 0.9897958 -0.1305392 0.0653042 0.1341776 0.9888031 -3.7327 2.8933 -55.126 dynamics C:\JOEL\SN1.snp mol 1 atom 1 - C C4 - -0.1983948 0 2.980232e-008 0 4 2 s 3 s 4 s 5 s vel 1 30.25053 -2.302274 -0.2019631 atom 2 - C C4 - -0.2030025 -0.5280889 1.047218 0.9847533 4 1 s 6 s 7 s 8 s vel 2 -36.75871 -3.031793 -4.924872 atom 3 - C C4 - -0.2109494 -0.6076289 -1.262611 0.4831286 4 1 s 9 s 10 s 11 s vel 3 -30.68537 -3.930437 -0.5878429 atom 4 - C C4 - -0.2069764 -0.299786 0.3162583 -1.43066 4 1 s 12 s 13 s 14 s vel 4 -26.39541 -3.084821 3.001078 atom 5 - I I - 0.05109215 2.053678 -0.07855448 0.09350133 1 1 s vel 5 44 -2.449861 0.4780697 atom 6 - H H - 0.07939154 -0.03756595 2.024587 0.8345751 1 2 s vel 6 7.50461 11.84373 -14.09784 atom 7 - H H - 0.07778263 -1.549778 1.267665 0.8610347 1 2 s vel 7 4.39162 3.01684 26.61516 atom 8 - H H - 0.08630878 -0.3687739 0.7196702 1.99503 1 2 s vel 8 -8.24415 -26.36442 -6.73903 atom 9 - H H - 0.08432347 -0.275228 -2.138733 -0.1791216 1 3 s vel 9 -2.41705 2.418344 -16.15356 atom 10 - H H - 0.09060758 -0.3526009 -1.53671 1.519861 1 3 s vel 10 2.44711 -22.56644 -0.455679 atom 11 - H H - 0.08138108 -1.718877 -1.143547 0.4530481 1 3 s vel 11 -16.34131 -30.99707 -13.37337 atom 12 - H H - 0.08636165 -0.09119892 -0.5958796 -2.063218 1 4 s vel 12 -17.62466 -10.93421 -8.909492 atom 13 - H H - 0.07858056 -1.333887 0.494966 -1.432124 1 4 s vel 13 8.51855 -14.12036 2.78491 atom 14 - H H - 0.1034942 0.3256751 1.177509 -1.85832 1 4 s vel 14 -16.95071 7.3233 2.475825 endmol 1 mol 2 atom 1 - Cl ** - 0 9.150539 -7.550364 -0.3907619 0 vel 1 -30.99183 28.34619 0 endmol 2 ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jan 16 19:59:28 1996 Date: Tue, 16 Jan 96 15:44 +0200 From: To: amber@cgl.ucsf.edu, anneal@chaco.com, c2-l@msi.com, CAChe@pacificu.edu, charmm-bbs@emperor.harvard.edu, chem-comp@mailbase.ac.uk, watoc@ic.ac.uk, chemistry@infomeister.osc.edu, chem-mod@mailbase.ac.uk, dibug@comp.bioz.unibas.ch, hyperchem@hyper.com, isisforum-l@mdli.com, mmodinfo@uoft02.utoledo.edu, pmd@cumbnd.bioc.columbia.edu, quanta-l@msi.com, sybyl@extreme.chem.rpi.edu, anchodd@cc.utas.edu.au, mmodlist@chem.iupui.edu Subject: WATOC96 The following is taken from the brochure for WATOC '96. Those who wish to receive the brochure should write to watoc96@vms.huji.ac.il ASAP. The registration forms may be filled also on the WATOC server- URL http://www.ch.ic.ac.uk/watoc_israel.html (starting approx. January 16) You may also print the appropriate forms from this text, complete them and mail to the Secretariat. The registration form is at about the middle of the following brochure (~line 500), after "transportation to Jerusalem" and before "complimentary congress tours" ---------------------------------------------------------------------- FOURTH WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS - WATOC '96 JERUSALEM, ISRAEL, JULY 7 - 12, 1996 CALL FOR PAPERS AND REGISTRATION BROCHURE DEADLINE FOR THE SUBMISSION OF ABSTRACTS: APRIL 15, 1996 --------------------------------------------------------- INTERNATIONAL SCIENTIFIC COMMITTEE M. Berman, Israel C. Cohen, Switzerland P. Gund, USA P. Hiberty, France J. Michl, USA V. Minkin, Russia E. Osawa, Japan L. Radom, Australia H.F. Schaefer III, USA P.v.R. Schleyer, Germany H. Weinstein, USA NATIONAL ORGANIZING COMMITTEE Y. Apeloig, Technion - Israel Institute of Technology, Haifa Chairman of Program Committee D. Arad, Tel Aviv University D. Gibson, The Hebrew University of Jerusalem A. Goldblum, The Hebrew University of Jerusalem S. Hoz, Bar-Ilan University, Ramat Gan D. Kost, Ben-Gurion University of the Negev, Beer-Sheva S. Lifson, The Weizmann Institute of Science, Rehovot S. Shaik, The Hebrew University of Jerusalem CONGRESS CHAIRMAN Prof. A. Goldblum Dept. of Pharmaceutical Chemistry, School of Pharmacy The Hebrew University of Jerusalem Jerusalem, Israel 91120 Tel: 972 2 758701; Fax: 972 2 410740 E-mail: amiram@vms.huji.ac.il CONGRESS ORGANIZERS AND SECRETARIAT Kenes Organizers of Congresses and Tour Operators Ltd. P.O. Box 50006, Tel Aviv 61500, Israel Tel: 972 3 5140000; Fax: 972 3 5175674 / 5140077 E-mail: watoc@kenes.ccmail.compuserve.com E-mail for Compuserve users: ccmail:watoc@kenes ---------------------------------------------------------------------- LETTER TO PARTICIPANTS Dear Colleague, On behalf of the Local Organizing Committee we take great pleasure in inviting you to join us in Jerusalem in July 1996 for the 4th Congress of the World Association of Theoretically Oriented Chemists. The purpose of the Congress is to bring together scientists interested in the development of various theoretical and computational methods, including molecular modeling, and their application to organic, inorganic, organometallic, biochemical, and biomedical problems. The WATOC Congress also aims to attract experimentalists who may wish to employ computational methods in their research. We and our colleagues in the National Organizing Committee are proud to host this important international meeting, to take place in the unique setting of Jerusalem, spiritual center of the three monotheistic religions. The city has a remarkable blend of the ancient - with its numerous holy and historical sites, and the modern - the beauty and convenience of a new city with the best tourist facilities. Jerusalem offers unforgettable views and visits to world-famous sites: the Western Wall, the Dome of the Rock, the Church of the Holy Sepulchre and Via Dolorosa, as well as many more. This year Jerusalem celebrates its 3000th anniversary which is marked by many special events. We hope that you will join us and take the opportunity to participate in the exciting scientific program, as well as to travel throughout this unique land. A specially-arranged program of tours will enable you to visit archaeological and holy sites throughout Israel, including Christian sites in the Galilee, as well as neighboring Egypt and Jordan. A visit to the Red Sea resort of Eilat offers remarkable coral reefs, water-sports and relaxation and a visit to the Dead Sea (the lowest spot on earth) and Masada is a unique experience. We look forward to welcoming you to a stimulating meeting and wish you an enjoyable stay in Jerusalem and in Israel. Yitzhak Apeloig Amiram Goldblum Chairman of Program Committee Congress Chairman --------------------------------------------------------------------- PRELIMINARY TIMETABLE SUNDAY, JULY 7, 1996 Afternoon: Registration and distribution of Congress material General WATOC Meeting Evening: Informal Welcome Reception MONDAY, JULY 8, 1996 Morning: Opening Ceremony and Award of WATOC Prizes All day: Congress Sessions Evening: Poster Session TUESDAY, JULY 9, 1996 Morning and afternoon: Congress Sessions Late Afternoon and Evening: Tour of Jerusalem and Visit to the Israel Museum WEDNESDAY, JULY 10, 1996 Morning: Congress Sessions Afternoon: Tour of Jerusalem Evening: Poster Session THURSDAY, JULY 11, 1996 All day: Congress Sessions Evening: Banquet (optional) FRIDAY, JULY 12, 1995 Morning: Congress Sessions and Closing Ceremony Afternoon: Optional Post-Congress Tours ------------------------------------------------------------------------ CONGRESS TOPICS Research on all aspects of computational chemistry is appropriate for presentation at the Congress. The Program will consist of Plenary Lectures, Invited Talks, Oral Presentations and Poster Sessions (including an electronic Poster Session). Congress Sessions will be roughly divided according to the three main topics below: * DEVELOPMENT OF THEORETICAL METHODS: AB INITIO, SEMIEMPIRICAL, FORCE FIELDS, DENSITY FUNCTIONAL, PSEUDOPOTENTIALS, VALENCE-BOND, ELECTRON CORRELATION, PERTURBATION THEORY, ETC. * APPLICATIONS IN ORGANIC, INORGANIC, AND ORGANOMETALLIC CHEMISTRY: ELECTRONIC STRUCTURE, REACTION MECHANISMS, CATALYSIS, SOLVENT EFFECTS, PHYSICO-CHEMICAL MEASUREMENTS (NMR, IR, UV, ETC.), MOLECULAR PROPERTIES, FRONTIER ORBITALS, CONFORMATIONAL ANALYSIS, THERMODYNAMICS AND KINETICS, ETC. * BIOCHEMICAL/BIOMEDICINAL THEORY AND APPLICATIONS: PROTEIN STRUCTURE/FUNCTION, ENZYME ACTIVITY AND MECHANISMS, NUCLEIC ACIDS, MEMBRANES, RECEPTOR STRUCTURE/FUNCTION, PROTEIN- DNA INTERACTIONS, CARBOHYDRATES, MOLECULAR DYNAMICS, MONTE- CARLO, QUANTUM MECHANICAL/MOLECULAR MECHANICS CALCULATIONS, SOLVATION, DRUG DESIGN, ETC. PLENARY LECTURERS T. Blundell D. Cremer W. F. van Gunsteren K.N. Houk P. Kollman W. Kutzelnigg K. Morokuma J.A. Pople H. Schwarz S. Shaik W. Thiel F. Weinhold H. Weinstein INVITED SPEAKERS J. Almlof D. Avnir T. Bally M.V. Basilevsky M. Berman F. Bernardi J. Bertran J. Brickmann W.T. Borden C. Cohen T. Clark I.G. Czismadia D.S. Dudis R. Elber G. Frenking J. Gauss J. Gerrat P.M.W. Gill R. Grev W.J. Hehre P.C. Hiberty S. Hoz A. Itai U. Kaldor M. Karni W. Koch D. Kost P. Lam R. Lavery G.H. Loew J.P. Malrieu K. Merz V. Minkin K. Muller S. Nagase E. Osawa S.D. Peyerimhoff A. Pross P. Pyykko L. Radom G. Richards H. Rzepa A. Sali J. Sauer H.F. Schaefer III H.B. Schlegel P.v.R. Schleyer B. Schoichet P. Schwerdtfeger G. Scuseria J. Skolnick R. Sustmann A. Warshel ------------------------------------------------------------- GENERAL INFORMATION An internet site for the Congress is at URL: http://www.ch.ic.ac.uk/watoc_israel.html. Please examine it regularly for updates. VENUE The Holiday Inn Crowne Plaza, Jerusalem 91130, Israel Tel: 972 2 6588888; Fax: 972 2 6514555. DATES Sunday, July 7 - Friday, July 12, 1996. LANGUAGE The official language of the Congress is English. REGISTRATION FEES until April 15, 1996 after April 16, 1996 Participant US$400 US$450 WATOC Member US$370 US$420 Student US$100 US$120 Accompanying Person US$150 US$150 Fees for PARTICIPANTS and STUDENTS include: participation in scientific sessions, Congress program and book of abstracts, invitations to the Congress tours and social events (excluding the Banquet on Thursday, July 11). Fees for ACCOMPANYING PERSONS include: two half-day tours and invitations to the Congress tours (two afternoons) and social events (excluding the Banquet on Thursday, July 11). You may register for the Congress using the enclosed form, or with the appropriate form on the WATOC Internet server. CANCELLATION POLICY Refund of registration fees will be made as follows: Airmail post-marked* before May 15, 1996 - full refund less US$40 (for handling expenses). Airmail post-marked* after May 15 until June 7 - 75% refund. Airmail post-marked* after June 8 - 50% refund. * or faxed, or electronically mailed VISAS Visas are guaranteed to all bona fide scientists. A visa to Israel is not necessary for participants from most countries (e.g., USA, Western Europe), but we suggest that you consult your travel agent. For participants from countries without diplomatic relations with Israel, please write directly to the Secretariat no later than TWO MONTHS prior to the Congress giving the following details: full name, date and place of birth, passport number and date and place of issue and expiry date, flight details (arrival date and flight number). The Secretariat will arrange for a visa to await you at Ben-Gurion Internatioanl Airport. LETTER OF INVITATION On request the Secretariat of the Congress will be happy to send a personal invitation to participate. It should be understood that such an invitation is only meant to help participants to raise travel funds or obtain a visa. It is not a commitment on the part of the organizers to provide any financial support. CALL FOR PAPERS The Scientific Committee welcomes scientific contributions dealing with any of the Congress main or related topics. Participants who wish to present papers are requested to submit an abstract to the Secretariat no later than April 15, 1996. Submittal of more than one abstract is wellcome. Abstracts submitted after this date may be scheduled for poster presentation, but their inclusion in the Abstract Book cannot be guaranteed. Scheduling and publication in the Congress publications is dependent on the payment of Registration Fees. For guidelines regarding the preparation of Abstracts please see the appropriate page. WATOC ELECTRONIC POSTERS An electronic poster session will be part of WATOC '96 and will begin one month before the Congress. The Chairman of the poster session is Professor Henry Rzepa of Imperial College, London. Professor Rzepa maintains and updates the WATOC server, and all abstracts for the electronic posters should be submitted through the appropriate form on that server. The URL of the server is http://www.ch.ic.ac.uk/watoc For abstracts submission, the URL is http://www.ch.ic.ac.uk/watoc/abstracts/abstract-form.html Help for submitting an electronic poster may be found under http://www.ch.ic.ac.uk/watoc/posters.html All abstracts for the electronic poster session should be submitted not later than April 15, 1996. They will undergo regular refereeing before being mounted for the electronic Conference. Abstracts to the electronic conference that are submitted by non-registered participants will not appear in full form in the book of abstracts of WATOC '96. However, abstract titles, authors and URL addresses of the electronic posters will be included in the Congress Book of Abstracts. PROCEEDINGS All oral presentations will be published, following regular journal refereeing, in a special issue of the Journal of Molecular Structure (Theochem) which publishes regularly all the plenary and invited lectures of WATOC conferences. Please indicate on the registration form if you are interested in purchasing the Proceedings. The proposed price for participants is DFl. 175,- (approx. US$120). SCHOLARSHIPS A limited amount of funding may be available for young scientists. Applications should be made directly to the Chairman. CLIMATE The weather in Jerusalem in July is warm and dry during the day, and cooler at night. Rain in July is a miracle! Temperatures range between 27 C (81 F) during the day and 17 C (63 F) at night. CLOTHING Informal for all occasions. We suggest that you bring sunglasses, a hat, comfortable walking shoes and a swimsuit. A light jacket may be useful for the evening. OFFICIAL CARRIER El Al Israel Airlines is the official carrier for the Congress. ------------------------------------------------------------------------------ TRAVEL AND ACCOMMODATION KENES TOURS P.O. Box 50006, Tel Aviv 61500, Israel Tel : 972 3 5140014 Fax : 972 3 5140044 / 5175674 Kenes Tours is the official travel agent for the Fourth World Congress of Theoretically Oriented Chemists and will be offering specially reduced rates for accommodation and Congress Tours. Hotel space has been reserved by Kenes Tours at the following hotels: Per person in a Single Room double room one person DELUXE CLASS Holiday Inn Crowne Plaza* Regular Room US$ 91 US$166 Crowne Club Room** US$117 US$216 SUPERIOR CLASS Park Plaza Hotel US$ 46 US$ 86 TOURIST CLASS Jerusalem Gate US$ 45 US$ 84 Tirat Bat-Sheva US$ 41 US$ 76 * Congress venue ** Crowne Plaza Club rooms include access to the Executive Floor Lounge. All above hotels are located within walking distance of the Congress venue except the Tirat Bat-Sheva hotel which is located in the city center with a regular bus service to the Congress venue. Rates are per night, per person including a large Israeli buffet style breakfast and service charge. STUDENT DORMITORIES A limited number of rooms has been reserved at the Hebrew University student dormitories, approximately 4 km from the Congress venue. Regular bus service to the Congress venue is available. Prices are US$20 per person in a double room, US$25 per person in a single room. Prices do not include breakfast. Applications should be made to the Secretariat. YOUTH HOSTELS Prices are between US$18-US$28.00 per person, per night, including breakfast. For reservations, please write directly to: 1. Israel Youth Hostels Association Convention Center, 1 Shazar St., Jerusalem 91060, Israel. Tel: 972 2 6558400; Fax: 972 2 6558432 2. Beth Shemuel Hostel. 6 Shamah St., Beth Shemuel, Jerusalem 94101, Israel Tel: 972 2 203456; Fax: 972 2 203467 Regular bus service to the Congress venue is available. HOW TO BOOK In order to benefit from the special congress rates, kindly send the enclosed Accommodation Form with the required deposit (see below) by AIRMAIL at your earliest convenience. You may also reserve accommodation for the Congress using the appropriate form on the WATOC Internet server. Reservations will be confirmed on a 'first come first served' basis. PAYMENT Payment of services (less deposit) should be made at the Kenes Tours Hospitality Desk upon registration. Kenes Tours accepts Travelers' cheques and Eurocheques (in the currency of the issuing country), Visa, MasterCard, American Express and Diners Club credit cards. Payment in Israeli currency is subject to Value-Added Tax which is currently 17%. IMPORTANT NOTES * Participants requiring single rooms will be accommodated in double rooms for single occupancy, without additional charge. * Kenes Tours reserves the right to change the requested hotels to those of a similar grade or better. * Kenes Tours and their agents shall not be responsible for, and shall be exempt from, all liability in respect of any loss, damage, injury, accident, delay or inconvenience to any person, or his/her luggage or any other property, for any reason whatsoever, for any tourist services provided. * Personal travel and health insurance is highly recommended. * Official check-in time for hotels is 14:00 and check-out time is noon. CANCELLATION POLICY Up to May 15, 1996 - full refund less bank charges Up to July 1, 1996 - cancellation charge of $ 50.00 per room After July 1 - cancellation charge of one night accommodation at your selected hotel. AIRPORT ASSISTANCE All participants advising Kenes Tours of their flight details will be met by a Kenes representative and assisted inside the arrival hall at the Ben-Gurion terminal, upon arrival on Sunday, July 7, 1996. Transfers from the Airport to the Congress hotels can be arrranged on Sunday, July 7, 1996 or any other day at an additional cost of US$30.00 per person, on a car sharing basis. Please forward exact flight information at least three weeks prior to arrival if transfer is required. TRANSPORTATION TO JERUSALEM FROM BEN-GURION INTERNATIONAL AIRPORT For participants arriving at Ben-Gurion International Airport who have not booked their transfer in advance, the following transportation alternatives to Jerusalem are available: "Egged" buses leave the airport regularly for Jerusalem Central Bus Station, from 07.00 to 21.30. Buses run until 15.30 on Friday and service resumes at 18.15 on Saturday (payment in local currency, approximately US$5). "Nesher"(sherut) taxis leave the airport for Jerusalem hotels, 24 hours a day. Taxis are shared with other passengers and they leave only when all places are taken, and cost approximately US$15 per person (payment in local currency). Private taxis (24 hours a day). The fare is fixed and the price list is posted at the taxi station in the airport as well as with the drivers. The price is approximately US$50 per taxi (payment in foreign or local currency). -------------------------------------------------------------------------- FOURTH WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS - WATOC '96 JERUSALEM, ISRAEL, JULY 7-12, 1996 REGISTRATION FORM Please complete and return this form, together with your payment, to: Secretariat WATOC '96 P.O.Box 50006, Tel-Aviv 61500 Israel Tel: 972-3-5140000 or 972-3-5140014 Fax: 972-3-5175674 or 972-3-5140077 Identification -------------- -------------- Please complete this section accurately; the information you provide will allow us to correspond with you efficiently, and it will also be used for your delegate badge at the Congress. Participant (Please TYPE or PRINT IN BLOCK LETTERS) Surname______________________________________________________________________ Initials_____________________ First name __________________________________________________________________ Title [ ] Prof. [ ] Dr. [ ] Mr. [ ] Mrs. [ ] Ms. Department___________________________________________________________________ Institution _________________________________________________________________ Mailing Address [ ] Office [ ] Residence ------------------------------------------------- ------------------------------------------------- No.___________Street___________________________________Suite/Apt.____________ City____________________________State/Province_______________________________ Country_________________________Postal Code__________________________________ Telephone (office hours) Country/city/number_________________________________ Fax Country/city/number_________________________________ E-Mail Address_______________________________________________________________ Accompanying persons -------------------- -------------------- List only those individuals registering for the Accompanying Persons' Program: Surname______________________________First name_________________Title_________ Surname______________________________First name_________________Title_________ Surname______________________________First name_________________Title_________ Surname______________________________First name_________________Title_________ Registration Fees ----------------- ----------------- Please check the appropriate box/s Until April 15, 1996 After April 16, 1996 Participant [ ] US $400 [ ] US $ 450 WATOC Member [ ] US $370 [ ] US $ 420 Student [ ] US $100 [ ] US $ 120 Accompaning Person/s x____ [ ] US $150 [ ] US $ 150 Banquet [ ] US $ 50 [ ] US $ 50 Payment ------- ------- Please indicate amount enclosed and ensure that you send your fully completed registration form together with your payment: Total Fees: $_______________US Method of Payment ----------------- ----------------- Option 1: Credit Card - Payments will be charged in US $ [ ] Visa [ ] MasterCard [ ] Diners [ ] American Express Number_____________________________Expiry Date (month/year)___________________ Name as shown on card: Surname__________________________________First name___________________________ Signature________________________________Date (day/month/year)________________ For payment by Visa, please indicate home address if other than mailing No._____________Street_________________________________Suite/Apt._____________ City____________________________State/Province________________________________ Country_________________________Postal Code___________________________________ Option 2: Bank Transfer - with your name and address indicated on the reverse. If payment is made for more than one person or by a company - please make sure that all names are indicated and send fully completed regsitration forms together with a copy of the bank transfer. Please make drafts payable to: "WATOC '96" and send them to Bank Leumi Le'Israel, Gan Hair Branch, Tel Aviv, Israel, Account number 816-56027/73 Patam. Bank charges are the responsibility of the payee and should be paid in addition to the registration fees. Option 3: Cheque made payable to "WATOC '96" Enclosed cheque number__________________ Bank________________________________ _______________________________________________________________________________ Please include fully completed registration form Cancellation policy ------------------- ------------------- Refund of Registration fees will be made as follows: Post-marked* prior to May 15, 1996 - full refund less US$ 40 handling fee Post-marked from May 15 until June 7 - 75% refund Post-marked after June 8 - 50% refund * or faxed, or electronically mailed [ ] I am interested in ordering the Congress Proceedings (Dfl. 175 ~ US$ 120) DATE__________________ SIGNATURE________________________________________ ------------------------------------------------------------------------------ COMPLIMENTARY CONGRESS TOURS OF JERUSALEM All Congress participants and registered accompanying persons are invited to join the following half-day tours: TUESDAY, JULY 9, 1996 JERUSALEM LEGENDS BY NIGHT Begin your tour at Yemin Moshe, one of the first Jewish neighborhoods in Jerusalem outside the walls of the Old City. Wind through the alleyways of Nahalat Shiva and Ethiopia Street. Continue to the ultra-orthodox neighborhoods of Mea Shearim with a special stop at an all-night bakery. On to the street of the local Jewish open-air market of Mahane Yehuda and Ohel Moshe. Finish the tour with a scenic ride through the area of the Knesset (Israel's parliament) and a visit to the Israel Museum. WEDNESDAY, JULY 10, 1996 JERUSALEM THROUGH THE AGES Drive to the Haas Promenade for a breathtaking view of the ancient Jerusalem from the south, to understand its topography, and how it developed throughout the ages. Continue to Jaffa Gate, one of Jerusalem's gates from the Ottoman period. Walk through the Arab Bazaar to the rooftops of the Old City for an overview of the Christian, Jewish, Moslem and Armenian Quarters. From there on to the Jewish Quarter and visit the Broad Wall, part of Jerusalem's walls from the First Temple period. We also visit the Hurva Synagogue, the center of Jewish life in Jerusalem in the nineteenth century. Descend to the Western Wall for a brief stop and an overview of the Southern Wall excavations. Exit the Old City at the Dung Gate and drive back to the hotels. ACCOMPANYING PERSONS' TOURS Registered accompanying persons are invited to join the following two half-day tours: MONDAY, JULY 8, 1996 TEL MARESHA AND KIBBUTZ BET GUVRIN Depart the lobby of the Holiday Inn Crowne Plaza Hotel for a visit to the unforgettable city of Maresha, the ancestral home of King Herod. This rare opportunity beckons you to explore and excavate in one of the 5,000 man-made cave compelxes which contain frescoed tombs, underground oil presses and remains of impressive villas. Contine to Kibbutz Bet Guvrin, where a kibbutz member will explain their unique way of life. An opportunity to understand the contrasts between ancient and modern Israel. THURSDAY, JULY 9, 1996 IN THE FOOTSTEPS OF JESUS Walk the alleyways and see the exact sites that Jesus journeyed through during his final days in the Jerusalem of 2,000 years ago. The tour begins above David's Tomb in the Crusader Room of the Last Supper. >From this spot on Mount Zion we travel to the Mount of Olives and descend from this majestic spot via the many churches. We stop at the Garden of Gethsemane, where Jesus was betrayed and finish at the tranquil spot of Gordon's Calvary, the Garden Tomb. ---------------------------------------------------------------------------- PRE- AND POST-CONGRESS TOURS The following tours are being offered exclusively to Congress participants PRE-CONGRESS DAY TOURS A. SATURDAY, JULY 6, 1996 BETH SHEAN, NAZARETH, TIBERIAS including the Church of the Anunciation and Sea of Galilee Price per person: US$60.00 Includes entrance fees. B. SUNDAY, JULY 7, 1996 DEAD SEA AND MASADA Price per person: US$65.00 Includes entrance fees and visit to Ein Gedi Spa Pick-up and drop off for day tours will be from Congress Hotels C. WEDNESDAY, JULY 3 - SUNDAY, JULY 7, 1996 EGYPT TOUR - 4 NIGHTS/3 DAYS WEDNESDAY, JULY 3, 1996 Arrival Overnight: Deluxe hotel, Tel Aviv THURSDAY, JULY 4, 1996 Departure from Tel Aviv by Air Sinai flight to Cairo, arrival at approximately 12:00 hrs. Transfer to the Ramses Hilton hotel, Cairo for check in. Half day city tour of Cairo. Dinner and overnight: Ramses Hilton Hotel FRIDAY, JULY 5, 1996 Morning flight to Luxor for a full day tour of Luxor Evening return flight from Luxor to Cairo. Dinner and overnight: Ramses Hilton Hotel SATURDAY, JULY 6, 1996 Full day tour of the Pyramids Dinner and overnight: Ramses Hilton Hotel SUNDAY, JULY 7, 1996 Morning flight from Cairo to Tel Aviv Transfer from Ben Gurion International airport to Congress hotels in Jerusalem. Price: Per person in a double room: US$ 645 Single room : US$ 757 Price includes: One overnight including breakfast in a deluxe hotel in Tel Aviv Three overnights at the Ramses Hilton hotel, including breakfast and dinner Group transfers from Tel Aviv hotel to Ben-Gurion International airport Group transfer from Ben-Gurion International airport to Jerusalem Congress hotels Domestic round trip flight from Cairo to Luxor Airport transfer from and to the hotel in Cairo 2 and a half days of touring in an air-conditioned bus with the services of an English-speaking guide. Entrance fees as per itinerary, porterage Price does not include: Lunches International flight from Tel Aviv to Cairo and return - Current Air Fare is US$ 280.00 per person (for a round trip fare). Reservation can be made with your personal travel agent in your country or by Kenes Tours upon request. Participants wishing to arrive directly in Cairo on Wednesday, July 3 or Thursday, July 4, 1996 (instead of Tel Aviv) are kindly requested to advise Kenes Tours accordingly. POST-CONGRESS TOURS (TOURS D AND E CAN BE COMBINED) D. FRIDAY, JULY 12 - SUNDAY JULY 14, 1996 GALILEE TOUR - 2 NIGHTS FRIDAY, JULY 12, 1996 Capernaum, Beth Shean, Nazareth (including the Church of the Anunciation), Tiberias and Sea of Galilee Overnight: Kibbutz Hotel or similar SATURDAY, JULY 13, 1996 Mount Carmel - Haifa, Acre (Crusader Citadel), Caesarea (ancient Roman port city) Lunch: at Druze Village hosted by Druze family Overnight : Deluxe Hotel, Tel Aviv SUNDAY, JULY 14, 1996 Departure for homebound flights or Tour E Price: Per person in double room: US$ 275.00 Single room : US$ 390.00 Price includes: One overnight in a deluxe hotel in Tel Aviv, including breakfast One overnight in a kibbutz guesthouse including dinner and breakfast One lunch en route Two full days touring in an air-conditioned bus with the services of an English speaking guide Entrance fees as per itinerary, portage E. SUNDAY, JULY 14 - TUESDAY, JULY 16, 1996 JORDAN TOUR - 3 days/2 nights SUNDAY, JULY 14 Ajlun, Jerash, Amman Dinner and overnight: Forte Grand Hotel, Amman (or similar) MONDAY, JULY 15 Full day tour to PETRA Dinner and overnight: Forte Grand Hotel, Amman (or similar) TUESDAY, JULY 16 Morning departure from Amman Mount Nebo and Mataba Evening arrival in Tel Aviv Price: Per person in double room: US$457.00 Single room supplement: US$ 70.00 Price for Jordan Tour includes: Group transfers from Tel Aviv to Jordanian/Israeli border crossing Three days of touring in an air-conditioned bus with the services of an English speaking guide Two overnights in a deluxe hotel in Amman including breakfasts and dinners Entrance fees as per itinerary, porterage Price does not include: Lunches Israeli and Jordanian border taxes (approx. $26 per person) Visa to Jordan and departure transfers from Jerusalem after the tour Hotel accommodations in Israel after the tour IMPORTANT NOTE: A valid entry visa to Jordan should be obtained at the Jordanian embassy/consulate in your home country prior to your arrival to Israel. It is your responsibility to obtain this Jordanian visa, and a re-entry visa (if applicable) to Israel. TOUR RATES ARE BASED ON A MINIMUM OF 15 PARTICIPANTS PER TOUR ----------------------------------------------------------------------------- FOURTH WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS - WATOC '96 Jerusalem, Israel, July 7 - 12, 1996 ACCOMMODATION, TOURS AND ARRIVAL TRANSFER FORM Please TYPE or PRINT in BLOCK LETTERS and AIRMAIL to: KENES TOURS P.O.Box 50006, Tel Aviv 61500, Israel Tel : 972 3 5140004, Fax: 972 3 5140044/5175674 SURNAME __________________ FIRST NAME __________________________ ADDRESS _________________________________________________________ _________________________________________________________________ _________________________________________________________________ COUNTRY __________________ TEL NO. ____________________ FAX NO. ____________________________ E-MAIL ADDRESS_________________________________________________ TYPE OF ROOM REQUIRED: [ ] double [ ] single [ ] other __________________ * I will share my accommodation with __________________________________ I/We require hotel accommodation as follows: First choice: -------------------------------------- Second choice: ------------------------------------ Check-in date:__________Check-out date:_________ No. of Nights__________ TOURS : NO. OF SEATS [ ] A. Beth Shean, Nazareth, Tiberias, Saturday, July 6, 1996 ____________ [ ] B. Dead Sea and Masada, Sunday, July 7, 1996 ____________ [ ] C. Egypt Tour, July 3-7,1996 oSingle oDouble*____________ [ ] D. Galilee Tour,Fri-Sun, July 12-14, 1996 oSingle oDouble*____________ [ ] E. Jordan Tour,Sun-Tues, July 14-16, 1996 oSingle oDouble*____________ * I will share my accommodation with _______________________________ ARRIVAL TRANSFER : Arrival on _______________________ Airline/Flight _________________ at ____________ hours. [ ] Please arrange arrival transfer to Jerusalem Congress hotels at an additional cost of US$30.00 per person on a car sharing basis. HOTEL DEPOSIT : All requests for accommodation must be accompanied by a deposit of one night accommodation of your selected hotel per room. Please make cheque payable to Kenes Tours or charge deposit to credit card, as per below: [ ] Cheque enclosed [ ] Credit card __________________________________ Number _____________________________ Expiration Date________________ SIGNATURE __________________________ DATE ____________________ --------------------------------------------------------------------- FOURTH WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS - WATOC '96 Jerusalem, Israel, July 7 - 12, 1996 JORDAN TOUR FORM Please TYPE or PRINT in BLOCK LETTERS and AIRMAIL to: KENES TOURS P.O.Box 50006, Tel Aviv 61500, Israel Tel : 972 3 5140004, Fax: 972 3 5140044/5175674 Please complete the following information in order to facilitate your border crossing. Note that you should obtain an entry visa to Jordan prior to your arrival in Israel. FULL NAME AS IN PASSPORT:_________________________________________ NATIONALITY:_____________________________________________________ PASSPORT NUMBER:________________________________________________ DATE PASSPORT ISSUED:_____________________________________________ DATE PASSPORT EXPIRES:____________________________________________ DATE OF BIRTH:____________________________________________________ Please complete the above form for each person participating in the Jordan Tour. Kindly note that it is your responsibility to check if you require and to obtain a re-entry visa to Israel. If you would like to arrange accommodation on your return to Israel, please specify when booking your tour. Hotel space has been reserved in the Carlton Hotel, Tel Aviv at the following special rates: o Double Room: (two people) US$194.00 o Single Room: (one person) US$158.00 Above rates are per room, per night including Israeli buffet breakfast. --------------------------------------------------------------------- ABSTRACTS INFORMATION FORM DEADLINE FOR THE RECEIPT OF ABSTRACTS: APRIL 15, 1996 Please state below the name, address and title of presenting author: FAMILY NAME___________________________________________________ FIRST NAME______________________________________________________ TITLE____________________________________________________________ ADDRESS_________________________________________________________ _________________________________________________________________ ________________________________________________________________ COUNTRY________________________ FAX____________________________ TELEPHONE NUMBER_______________________________________________ E-MAIL ADDRESS__________________________________________________ I wish to submit the enclosed abstract for [ ] oral [ ] oral and video [ ] poster presentation 1. Abstracts should be typed on plain white paper in a rectangle 17cm x 23cm. The entire abstract, including title, author(s), institution(s), country and acknowledgments must fit within the rectangle. 2. Abstracts will be printed exactly as submitted. Font size should be equal or larger than 10 pts. Abstracts should be typed on an electric typewriter or be of print quality out-put. A dot-matrix printout is not acceptable. 3. Capitalize and do NOT indent title. Title should be followed by author(s)' name(s) on a separate line and, on the following line - institution, city and country. First names or initials must precede last name. Leave one line between the title and the author's names. Underline the name of the presenting author. Begin body of the abstract on a new line and indent five spaces. 4. PLEASE DO NOT FOLD OR FAX YOUR ABSTRACTS 5. Abstracts should be sent with five (original and four copies) copies to: Secretariat WATOC '96, P.O. Box 50006, Tel Aviv 61500, Israel _______________________________________________________________ Prof. Amiram Goldblum Chairman of WATOC '96 Phone 972-2-758701 Hebrew University of Jerusalem FAX 972-2-410740 School of Pharmacy email watoc96@vms.huji.ac.il Jerusalem 91120 ISRAEL ________________________________________________________________ ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jan 17 06:50:12 1996 Date: Wed, 17 Jan 1996 07:51:46 +0200 To: hyperchem@hyper.com From: kostd@bgumail.bgu.ac.il (Daniel Kost) Subject: Constraining parameters during optimization Hi Hyperchemers, Here is a problem I have been troubled with. It is easy to constrain bondlengths and angles during optimization to a desired (invariant) value. But what if the distance you want to hold constant is not along a "real" bond? how about the distance between two molecules, expressed in terms of the distance between two individual atoms on each molecule? I could not fool the system to hold these distances (or angles) constant. Any suggestions on how one might accomplish this? I hope this is not just another trivial question. Thanks for your comments/answers Daniel Kost ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jan 17 15:06:34 1996 Date: Wed, 17 Jan 96 10:00:24 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: Re: Constraining parameters during optimization > Date: Wed, 17 Jan 1996 07:34:53 +0200 > From: kostd@bgumail.bgu.ac.il (Daniel Kost) > > Here is a problem I have been troubled with. It is easy to constrain > bondlengths and angles during optimization to a desired (invariant) value. > But what if the distance you want to hold constant is not along a "real" > bond? how about the distance between two molecules, expressed in terms of > the distance between two individual atoms on each molecule? I could not > fool the system to hold these distances (or angles) constant. Sure you can, exactly the same as if the distance is within a single molecule. Select the two atoms, name the selection, and then use that name in Setup/Restraints. Specify the distance you want, specify the force constant -- 20 mdyne/A is moderate, 50 mdyne/A is rather rigid. 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 Jan 17 17:26:42 1996 Date: Wed, 17 Jan 1996 12:25:51 -0500 (EST) From: "William T. Winter" To: Daniel Kost Cc: hyperchem@hyper.com Subject: Re: Constraining parameters during optimization Here is a method that should work in molecular mechanics forcefields. Create a new atom type(s) for the atom(s) whose long range distance you want to constrain. Change the atom types in your *.hin file and run a single point calculation. The error messages will identify the terms involving your new atom type which are not defined. Add additional lines to the relevant source file (for ambers they would be files of the form am90s*.txt) For example if two CS type atoms were changed to new type C9, the you might want to add a line in file am90sstr.txt for CS -C9 which would have the same values as for CS-CS etc. Then in am90snbd.txt add a new line for C9 where the first term is 1/2 of your desired distance in angstroms and the second is some fairly large weight (this will have to be adjusted for suitable results) . Recompile the force field and minimize. If your distance is too far from the desired value, increase the weight in the nonbonded file. This is of course a totally subjective approach to building in one or a few long range distances. Now what would be really nice would be the ability to restrain a model to a particular helical geometry as we do in our own LALS program. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 URL http://www-chem.esf.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jan 18 09:03:10 1996 From: kreidler@iris.rz.uni-duesseldorf.de (Kay Kreidler) Subject: scripts and macros To: hyperchem@hyper.com Date: Thu, 18 Jan 1996 08:33:20 +0100 (MET) Dear Hyperchem Users! I have a question concerning the use of an Excel macro / script not to write out the energy of a molecule but specific dihedral angles. Is it possible to read in a nunmber of files, mark a few specific dihedral angles and write the results into for example an Excel sheet? Another question is about generating conformations and writing filenames. I'd like to generate starting conformations of a molecule containing an ethan rotator with increments of the dihedral angle of for example 10 degrees. But because of using a different program than Hyperchem for the calculation, I just want Hyperchem to write out the file names of the different conformations with a variable file name, eg 01.zmt, 02.zmt, ... Is this possible with any kind of script? I hope, my question is comprehensive. I searched the archives of the list, but didn't find anything. Thanks for your help. Kay. Kay Kreidler Department of Inorganic and Structural Chemistry Heinrich-Heine-University Duesseldorf Germany ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jan 18 13:53:34 1996 Date: Thu, 18 Jan 1996 20:00:22 +0900 From: Shigeo SUZUKI To: hyperchem@hyper.com Subject: Upgrade survice to foreign user I am a foreign HyperChem/ChemPlus user. Japanese HyperChem suuplier (KGT Co.) anounced the upgrade survice to HyperChem Release 4.5 in last year. But the ChemPlus upgrade could not be avilable. Can I get upgrade survice of HyperChem and also ChemPlus directly from you? Please inform me! Sincerely _/_/_/ Shigeo SUZUKI (Pharm. Sci., Kinki Univ.) _/_/_/ _/_/_/ e-mail: suzuki@phar.kindai.ac.jp _/_/_/ ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jan 18 16:27:10 1996 Date: Thu, 18 Jan 96 11:01:22 -0500 From: polowin (Joel Polowin) To: hyperchem@hyper.com Subject: Re: scripts and macros > From: kreidler@iris.rz.uni-duesseldorf.de (Kay Kreidler) > Date: Thu, 18 Jan 1996 08:33:20 +0100 (MET) > > I have a question concerning the use of an Excel macro / script not to > write out the energy of a molecule but specific dihedral angles. Is it > possible to read in a nunmber of files, mark a few specific dihedral > angles and write the results into for example an Excel sheet? Yes. The sample macro PLOT.XLM, which is supplied with HyperChem for Windows, can show you how to read in files one by one. If the dihedral angles are already set up as named selections and you know the names in advance, you could include the selection names in other cells in the spreadsheet page and use them with the 'select-name' command to select them one by one. For each, the 'named-selection-value' command will return the value (in this case the torsional angle); this can be put into the spreadsheet, again as shown in PLOT.XLM . If the selections are named but you do not know the names in advance, the process of getting the values is more complex. You would use 'named- selection-count' to get the number of named selections, and then use that in a loop, using the 'named-selection-name' command to get each selection name. For each, the 'select-name' command can be used to select it. Then to see if you have a torsion angle, you can find out if 'selected-atom-count' is 4, and you can get the value of 'status- message' to find out if it includes the word "improper". (That lets you find out if you have a torsion angle or an 'improper torsion angle'.) If it is a torsion angle, you then get and save the value of 'named- selection-value'. > Another question is about generating conformations and writing filenames. > I'd like to generate starting conformations of a molecule containing an > ethan rotator with increments of the dihedral angle of for example 10 > degrees. > > But because of using a different program than Hyperchem for the > calculation, I just want Hyperchem to write out the file names of the > different conformations with a variable file name, eg 01.zmt, 02.zmt, ... In general, this is simple enough; it is pretty much like the process for reading in a series of file names except that you build the file names for saving out of a loop counter. This involves working with string variables and number formatting in Excel. I suggest that you download the macros that are available on our ftp site (ftp.hyper.com , in /pub/macros ) or our WWW site (see below) and study how they work. This should put you well on your way to writing your own macros. 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 Tue Jan 23 02:01:56 1996 From: XIENING@Meena.CC.URegina.CA Date: Mon, 22 Jan 1996 19:55:50 -0600 (CST) Subject: help To: hyperchem@hyper.com hi, hyperchemers, I am a new user of hyperchem. In our lab we have three computers on which hyperchem is installed. But hyperchem doesn't seem work properly on one of them because everytime I run hyperchem, it gives a warning like: parallel port lock must be installed in order to operate hyperchem. Is there anybody out there who can help me with it? What is so-called "parallel port lock" and how to install it? I will appreciate any reply. Thanks. ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jan 23 15:35:40 1996 From: "Steven Desjardins" Organization: Washington & Lee University To: hyperchem@hyper.com Date: Tue, 23 Jan 1996 08:48:42 EDT Subject: HyperChem Lite I would like info about HyperChem Lite. (Features, Prices,etc.). I tried the Web site but couldn't find anything. Thanks. Steven G. Desjardins Department of Chemistry Washington and Lee University Lexington VA 24450 (703) 463-8873 ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jan 23 15:46:14 1996 Date: Tue, 23 Jan 1996 13:13:59 GMT To: chemistry@infomeister.osc.edu, chem-mod%mailbase@ac.uk, dibug@comp.bioz.unibas.ch, hyperchem@hyper.com, isisforum-l@mdli.com, mmodinfo@uoft02.utoledo.edu, pmd@cumbnd.bioc.columbia.edu, quanta-l@msi.com, sybyl@extreme.chem.rpi.edu, anchodd@cc.utas.edu.au, mmodlist@chem.iupui.edu From: Didier Rognan Subject: Second Swiss Course on Medicinal Chemistry Second Swiss Course on Medicinal Chemistry 6-11 October 1996, Leysin, Switzerland organized by the Section of Medicinal Chemistry of the New Swiss Chemical Society SCOPE OF THE COURSE The course on medicinal chemistry offers to young scientists with a few years of experience in the pharmaceutical industry and interested Ph.D. students a broad overview of disciplines involved in modern preclinical drug research. The development of integrative abilities is a prerequisite to function in todays multidisciplinary drug discovery teams. The course is set up for synthetic organic chemists, as well as biologists and pharmacologists and those involved in drug design and the physicochemical characterization of biologically active compounds. Active participation by the participants in tutorials and the presentation of three case histories are important parts of the course. PROGRAMME AND LECTURERS=09 What is medicinal chemistry? Prof. B. Testa (Uni. Lausanne, CH) =09 Molecular & Cell Biology=09 What are the targets for the medicinal chemist Dr. W. Schilling (Ciba, Basle - CH) Introduction to molecular biology Prof. T.H. Schwartz (Uni. Copenhagen, DK) Integration of molecular biology with medicinal chemistry Prof. T.H. Schwartz (Uni. Copenhagen, DK) Introduction to molecular immunology Dr. J.-Y. Bonnefoy (Glaxo, Geneva - CH) =09 Lead Finding & Development=09 Lead discovery Dr. M. Sills (Ciba, Summit - USA) Introduction to combinatorial chemistry Dr. E. Feder (Ciba, Basle- CH) Developing a lead Dr. D. Roberts (Zeneca, Macclesfield - UK) Patents and regulatory apects Dr. R. Ross (Sandoz, Basle - CH) =09 Pharmacodynamics=09 Principles of pharmacological assays Prof. H. M=F6hler (Uni. Z=FCrich, CH) Ion channels as drug targets Prof. U. Quast (Uni. T=FCbingen, D) =09 Phamacokinetics, Toxicology & Drug Delivery=09 Introduction to pharmacokinetics Prof. H. Spahn-Langguth (Uni. Halle, D) Introduction to drug metabolism Prof. B. Testa (Uni. Lausanne, CH) Introduction to molecular toxicoloy Prof. N.P.E. Vermeulen (Uni. Leiden, NL)= =20 Formulation and drug delivery Prof. D. Crommelin (Uni. Utrecht, NL) =09 Molecular Design & Lead Optimization=09 Physicochemical concepts and drug absorption Dr. H. van de Waterbeemd (Roche, Basle - CH) Molecular modeling Prof. G. Folkers (ETH Z=FCrich, CH) Computer-assisted lead optimization Prof. H. Kubinyi (BASF, Ludwigshafen -= D) =09 Case Histories=09 Development of aromatase inhibitors Prof. A. Bhatnagar (Ciba, Basle - CH) The story of LESCOL Dr. F. Kathawala (Sandoz, East Hanover - USA) Development of INVIRASE Dr. J. Lawton (Roche, Welwyn - UK) =09 ORGANIZATION Prof. Gerd Folkers (ETHZ, chairman), Dr. H. van de Waterbeemd (Roche, vice-chairman)=20 Dr. W. Froestl (Ciba), Dr. R. Jakob-Roetne (Roche), Dr. D. Rognan (ETHZ), Prof. B. Testa (Uni. Lausanne), Dr. R. Wenger (Sandoz) WORLD WIDE WEB A description of the course including programme, location, accomodation facilities and registration form can be found at the following URL: http://www.pharma.ethz.ch/leysin PRACTICAL INFORMATIONS Location The course will be held at the Classic Hotel in Leysin, Switzerland. In the heart of the =93Alpes Vaudoises=93 and within easy reach of the towns of the Lake Geneva Region, Leysin is the perfect answer to the wishes and expectations of all those who love nature, winter and summer sports, walks, good food, the opportunity to meet interesting people, relaxation. =09 =09 Hotel The Classic is the largest hotel in Leysin, within the spirit of the resort. It offers a large array of single and double rooms, bars, restaurants, terrace, auditorium/cinema, gastronomic events. Registration fees=09 The individual fee of Sfr 2500,- includes hotel accomodation with breakfast, course documentation, coffee breaks, lunches and dinner. Students pay a special price of only SFr 250,- (please include justification to your registration) Registration The registration form should be returned before the end of April 1996. The course is limited to about 60 participants. Confirmation and payment instructions will be sent to all accepted participants. Late registrations after May 1st 1996 will require 10% additional fee.=09 =09 Arrival=09 Sunday October 11, 1996 in the afternoon. Welcome drink at 6 p.m. Language The official language of the course is English.=09 =09 ". . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .=20 REGISTRATION FORM Second Swiss Course on Medicinal Chemistry (6-11 October 1996, Leysin, Switzerland) Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . =20 Organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Address . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .=20 Zip Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . City . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Country . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Present function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .=20 Tel: . . . . . . . . . . . . . . . . . . . . . Fax: . . . . . . . . . . . . . . . . . . . . . E-mail: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Signature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Date . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Please return this form to:=20 Prof. Gerd Folkers, Dpt. of Pharmacy - ETH Wintherturerstrasse 190- CH-8057 Z=FCrich, Switzerland Tel. +41.1.257 60 60, Fax: +41.1.262 15 80, E-mail: folkers@pharma.ethz.ch Payments should be made to: Bankaccount 0061-867802-80-1 of Cr=E9dit Suisse Claraplatz, CH-4005 Basel, Switzerland. (Ref: Swiss Med Chem) ----------------------------------------------------------- Dr. Didier Rognan Department of Pharmacy - ETH Winterthurerstr.190, Room I17M50 CH-8057 Zuerich phone:+41.1.257 60 63 fax: +41.1.262 15 80 email: didier@pharma.ethz.ch www: http://www.pharma.ethz.ch/~didier ----------------------------------------------------------- ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jan 23 22:28:21 1996 Date: Tue, 23 Jan 1996 10:56:18 -0800 To: hyperchem@hyper.com From: "J.L. Beauchamp" Subject: Sodium Parameters for PM3 and AM1 Hyperchem users: Is anyone aware of the availability of parameters for sodium to be used in AM1 and PM3 semiempirical calculations? We are conducting experiments with the interaction of biopolymers (peptides and oligonucleotides) with lithium and sodium ions in the gas phase. Thanks for your help, J.L. Beauchamp J.L. Beauchamp California Institute of Technology 127-72 Pasadena, CA 91125 Phone: 818-395-6525 FAX: 818-568-8641 EMail: jlbchamp@cco.caltech.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jan 24 16:24:51 1996 Date: Wed, 24 Jan 1996 10:37:14 -0500 To: hyperchem@hyper.com From: "Dr. Paolo Mencarelli" Subject: HyperChem and Windows 95 Hi Since I am planning the conversion from Windows 3.1 to Windows 95, I would like to know how HyperChem run under Windows95. I am particularly interested about the velocity of execution. I was told that the old 16 bit applications run slower under Win95. Is that true? Thank Paolo =================================================== Dr. Paolo Mencarelli Dipartimento di Chimica - Universita' La Sapienza P.le Aldo Moro, 2 00185 Roma - ITALY tel 06-49913697 fax 06-490631 E-Mail p.mencarelli@caspur.it =================================================== ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jan 24 19:18:37 1996 From: CTARG@Levels.UniSA.Edu.Au Date: Wed, 24 Jan 1996 17:15:34 +0930 Subject: using Hyperchem in a Windows emulator To: hyperchem@hyper.com Hi, I'm trying to run my version of Hyperchem on a silicon graphics workstation using a Windows emulator - Softwindows. It seems to load OK and it seems to find the hardware lock. The most obvious problem at the moment is that the background is black but so are the icons representing the tool bar. Is there any way I can change the background to white by editing a Hyperchem file but not starting the program. The first order menus also show up i.e. for instance in setup, molecular mechanics etc... but the second order menus don't appear. For instance when I click on Molecular Mechanics I get the correct message on the bottom of the Hyperchem window but no menu appears and everything hangsup. Any suggestions? I started Hyperchem by clickin gon c60.hin and it loaded the structure OK so I think everything is functioning. There are obviously some default colours that have gone haywire somewhere. Can anybody help? Thanks Andrea ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jan 25 08:48:33 1996 From: cbrown@dhvx20.csudh.edu Date: Thu, 25 Jan 1996 01:23:11 PST To: hyperchem@hyper.com Subject: New user. Help. Dear HyperChem users Please forgive me, for I am a novice. I have just recently entered the world of HyperChem and I am having trouble modeling a structural motif. I have thoroughly combed the tutorial manual, so I am familiar with the terminology and the menus. I am trying to produce a leucine zipper coiled-coil structure, and I am not having any luck. If someone could please e-mail or fax me a protocol, or even suggestions, that would accomplish this task I would deeply appreciate it. The primary sequence of the peptide that I am working with is as follows: NNLLR AIEAQ QHLLQ LTVWG IKQLQ ARILA VERYL KDQ According to my reference material, a dimer of this peptide will produce a leucine zipper coiled-coil structure and can be modeled. Thanks in advance for the help, Craig Brown Charles Drew University of Medicine and Science fax: (310) 533-0244 e-mail: cbrown@dhvx20.csudh.edu cbbrown@earthlink.net ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Jan 25 17:00:22 1996 Date: Thu, 25 Jan 96 11:08:31 -0500 From: polowin (Joel Polowin) To: CTARG@Levels.UniSA.Edu.Au Subject: Re: using Hyperchem in a Windows emulator Cc: hyperchem@hyper.com > From: CTARG@Levels.UniSA.Edu.Au > Date: Wed, 24 Jan 1996 17:15:34 +0930 > > I'm trying to run my version of Hyperchem on a silicon graphics > workstation using a Windows emulator - Softwindows. It > seems to load OK and it seems to find the hardware lock. > The most obvious problem at the moment is that the background > is black but so are the icons representing the tool bar. > Is there any way I can change the background to white by editing a > Hyperchem file but not starting the program. You can change the background colour by editing the CHEM.INI file while HyperChem is not running. You would want to change the line that says "BackgroundColor=Black" so that it says "...=White", for example. I'm a bit surprised that the system is able to find the hardware lock. I suppose that SoftWindows for SGI can offer parallel-port support even though SoftWindows for Macs cannot (since Macs don't *have* parallel ports). > The first order menus also show up i.e. for instance in setup, > molecular mechanics etc... but the second order menus don't > appear. For instance when I click on Molecular Mechanics I get > the correct message on the bottom of the Hyperchem window > but no menu appears and everything hangsup. > Any suggestions? > > I started Hyperchem by clickin gon c60.hin and it loaded the > structure OK so I think everything is functioning. There > are obviously some default colours that have gone haywire somewhere. It sounds like you need to start by talking with the SoftWindows people, unless there are colour options that you can play with in the operating system. What about other "second-order menus" such as the ones under the Edit menu for Rotate, Translate, Set Bond Length, etc.? I can understand why the computation options make the system hang up, if for some reason the computational modules cannot be started or cannot communicate with the main program if they do start. If you really want to use HyperChem on your Silicon Graphics machine, I would suggest that you upgrade from the Windows software to the SGI version of HyperChem. Apart from the obvious advantages such as better graphics options, the software will run *much* more quickly without the need for Windows emulation. 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 Jan 25 17:44:49 1996 Date: Thu, 25 Jan 1996 09:54:23 -0800 From: "Harry R. Matthews" Organization: U.C. Davis To: hyperchem@hyper.com Subject: parallel port lock problems The parralell port lock strikes again! One of my hard drives crashed - not the one with HyperChem on it. However, when the drive was replaced I had to reinstall Windows NT 3.51 (service pack 3). Now, HyperChem claims there is no parallel port lock. (Yes, the printer is turned on.) Do I have to reinstall HyperChem? Other programs on the C: drive survived intact. Any help would be appreciated. -- Harry R. Matthews, Professor of Biological Chemistry, University of California at Davis, CA 95616, USA. 'phone 916 752 3570 / FAX 916 752 3516 email hrmatthews@ucdavis.edu www http://moby.ucdavis.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Fri Jan 26 17:01:33 1996 Organization: CNR - SIAM - Milano (Italy) Date: Fri, 26 Jan 1996 17:43:28 +0100 (MET) To: hyperchem@hyper.com From: ico@siam.mi.cnr.it (Istituto di Chimica degli Ormoni) Subject: Chromium Parameters Hi hyperchemers, problems comes from simple molecules. I am trying to minimize benzene chromium tricarbonyl (C6H6Cr(CO)3) without success. With MM and ZINDO the structure obtained are totally different from that one determined with X-ray. I try to use ab initio minimization with my P-90 16 Mb Ram but takes too long (more then one week). Any suggestion how to modify the force field for MM? There is a place in Internet where I can found such parameters? Tanks for your help, Gianluca OTTOLINA Istituto di Chimica degli Ormoni, CNR Milan, ITALY ________________________________________________________________________ From owner-hyperchem@hyper.com Fri Jan 26 19:20:03 1996 From: Dragan Vuckovic Subject: HyperChem Workshop - California To: hyperchem@www Date: Fri, 26 Jan 1996 15:07:24 -0500 (EST) Hypercube, Inc. presents an Introductory HyperChem Workshop on Computational Chemistry April 10 -12, 1996 Ready Serve Computer Center Santa Clara, California, USA HyperChem is like any other powerful tool: the more you know about it, the more you get out of working with it. For those who wish to learn more about the methods of molecular modeling and computational chemistry, about the ways of working with HyperChem, and about the range of problems you can now tackle on a PC, Hypercube, Inc. (the developers of HyperChem) offer an intensive three-day introductory workshop on molecular modeling with HyperChem. The workshop is pragmatic and application-oriented and makes no assumption of previous computational chemistry experience. Workshop Objectives The workshop will introduce you to techniques for working efficiently with HyperChem and other Hypercube's products, provide a pragmatic user's guide to the scientific methods behind HyperChem, and include many hands-on exercises based on practical molecular modeling problems. Workshop Outline Day 1. Morning: Overview of Computational Chemistry Techniques; HyperChem Graphical Interface Afternoon: Molecular Mechanics Methods Laboratory session Day 2. Morning: Approximate and Semiempirical Molecular Orbital Methods; Ab initio Molecular Orbital Methods Afternoon: Frontier Orbital Theory: Examining Molecular Reactivity; Laboratory session Day 3. Morning: Molecular Dynamics; Molecular Spectroscopy; QSAR/Group Contribution Methods Afternoon: Laboratory session (optional) Costs and Venue The cost for the three-day course is $995 US (Academic and Government discount price is $795 US). For early registration (before March 15) the price is $925 US ($725 US - academic). This covers the cost of course materials, coffee, lunches, and a PC to work on for the duration of the course (each participant will have his/her own machine). The number of participants is limited, so that extensive interaction with the workshop instructors is possible. Bring your own problems to work on during the course! The course will be held at the Ready Serve Computer Center, 5201 Great America Parkway, Suite 355, Santa Clara, California, USA. A map and a list of nearby reasonably-priced hotels will be sent to all participants upon registration. The participants are expected to make their own travel and accommodation arrangements. Registration To register for the Workshop, please complete the form and return as soon as possible to: Dr. Dragan Lj. Vuckovic Hypercube, Inc. Unit 7, 419 Phillip Street Waterloo, Ont. Canada N2L 3X2 e-mail: vuckovic@hyper.com Tel. (519) 725-4040 Fax: (519) 725-5193 Registration Form HyperChem Workshop on Computational Chemistry Santa Clara, California, USA April 10-12, 1996 Please reserve ____ spaces for the above workshop. NAME _______________________________________________________ ORGANIZATION _______________________________________________ POSITION ___________________________________________________ ADDRESS FOR CORRESPONDENCE ____________________________________________________________ ____________________________________________________________ ____________________________________________________________ TEL. NO. _______________________ FAX NO. ___________________ Fees payable in advance: I enclose a check for $__________ US Please make your check payable to Hypercube, Inc. Please invoice me: Purchase Order Number __________________ VISA Card No: ____________________________ Exp. Date: _________ Cardholder: ________________________________ Amount $________US SIGNATURE _____________________________ DATE ___________________ *Cancellation: If a participant cancels on or before March 27th (two weeks before the workshop), 50% of the workshop fee will be refunded. There will be no refunds for cancellations received after March 27, 1995. ___________________________________________________________________ Dr. Dragan Lj. Vuckovic phone: (519) 725-4040 International Marketing Manager fax: (519) 725-5193 Hypercube, Inc. e-mail: vuckovic@hyper.com 419 Phillip Street URL: http://www.hyper.com Waterloo, Ontario Canada, N2L 3X2 ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jan 29 06:36:29 1996 From: "Alexey A. Kubasov" Subject: help To: hyperchem@hyper.com Date: Mon, 29 Jan 1996 12:35:30 +0300 (GMT+0300) Need a Help. My scientific interests are catalysis and adsorption on zeolites and various oxides. Now I want to do semi-empirical calculations of some simple molecules (water,ethanol, ethylene) with fragments modeling zeolite structure. I know a little about Hyperchem and therefore I have some questions. 1. May I use HyperChem for such calculations (about 200 atoms)? 2. May I use Al and Si parameters build in the standard program or I ought to change them? 3. Where I may find proper parameters (InterNet or other) if it is necessary to change them? Excuse me for my poor English and Thank You in advance for the help. Alexey A.Kubasov Moscow State University Chemical Department Russia e-mail: kubasov@comp.chem.msu.su ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jan 29 06:36:36 1996 Date: Mon, 29 Jan 1996 09:48:37 +0000 To: hyperchem@hyper.com From: mesbah@thioiris1.ismra.fr (mesbah abdelhalim) Subject: Using SGI Hyperchem 2 with IRIX 5.3 Dear HyperChem users We have an SGI Hyperchem release 2, running under IRIX 4.0.5F. We are planing to upgrade the IRIX system to release 5.3. So, I am asking the following question : are there any problems, running SGI hyperchem 2 under IRIX 5.3 ? Tanks for your help, ***************************************************** MESBAH Abdelhalim Laboratoire de Chimie Moleculaire et Thio-Organiques ISMRA., URA. 480 CNRS 6, boulevard du Marechal Juin 14050 Caen Cedex, France T=E9l. 31 45 28 64 =46ax. 31 45 28 77 Email. mesbah@thioiris1.ismra.fr ***************************************************** ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Jan 29 16:22:40 1996 Date: Mon, 29 Jan 96 10:58:49 -0500 From: polowin (Joel Polowin) To: mesbah@thioiris1.ismra.fr (mesbah abdelhalim), hyperchem@hyper.com Subject: Re: Using SGI Hyperchem 2 with IRIX 5.3 > Date: Mon, 29 Jan 1996 09:48:37 +0000 > From: mesbah@thioiris1.ismra.fr (mesbah abdelhalim) > > We have an SGI Hyperchem release 2, running under IRIX 4.0.5F. We are > planing to upgrade the IRIX system to release 5.3. > So, I am asking the following question : are there any problems, running > SGI hyperchem 2 under IRIX 5.3 ? One big problem: it won't work at all. HyperChem v.2 for SGI is not compatible with Irix 5.x; it will work only with systems up to 4.0.5. When we put out the SGI back-ends, we had to produce different versions for the 4.0.5F and 5.2 operating systems, since they are neither upwards nor downwards compatible. You may wish to upgrade your old copy of HyperChem to the current Release 4.5 for SGI, which will run under IRIX 5.3 . I can send information about upgrading, or you can contact your local dealer. Information is also available from our WWW page (see below). 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 Jan 29 16:38:10 1996 Date: Mon, 29 Jan 96 10:45:17 -0500 From: polowin (Joel Polowin) To: "Alexey A. Kubasov" , hyperchem@hyper.com Subject: Re: help > From: "Alexey A. Kubasov" > Date: Mon, 29 Jan 1996 12:35:30 +0300 (GMT+0300) > > My scientific interests are catalysis and adsorption on zeolites > and various oxides. Now I want to do semi-empirical calculations > of some simple molecules (water,ethanol, ethylene) with fragments > modeling zeolite structure. I know a little about Hyperchem and > therefore I have some questions. > > 1. May I use HyperChem for such calculations (about 200 atoms)? Yes, in principle. Calculations of this size will probably require a lot of RAM and/or virtual memory (swap space) to run. You may need to increase the amount of RAM in your computer to get the calculations to run in reasonable time. > 2. May I use Al and Si parameters build in the standard program > or I ought to change them? If the parameters are present in the sets that we supply, they should be suitable for any purpose, I think. The situation is not the same as for molecular mechanics, in which atom parameters are optimised for specific chemical environments. > 3. Where I may find proper parameters (InterNet or other) if it > is necessary to change them? Asking on this mailing list is one possible source. Another is the Computational Chemistry mailing list -- to subscribe to that, write to the list coordinator at CHEMISTRY-REQUEST@ccl.osc.edu . Asking on the sci.chem newsgroup may also be useful. 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 Tue Jan 30 15:16:39 1996 From: "Thomas Futterer t4633" To: hyperchem@hyper.com Date: Tue, 30 Jan 1996 14:45:26 +0100 Subject: HyperChem Release 4.5 for SGI Dear Hyperchem users and developer, I have the new Relrase 4.5 for SGI. It seems to work properly. My questions: 1. Is it possible that HyperChem works in the background after I`ve logged out from the system? Now it doesn`t. 2. I have some ***.xyz files derived from x-ray studies. It is no problem to open the file, but the atoms are not connected automatically to get a molecule. Is there a way to this automatically. Thanks , Thomas Futterer ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jan 30 17:46:41 1996 From: Dragan Vuckovic Subject: HyperChem User Group Meeting - 1996 To: hyperchem@www Date: Tue, 30 Jan 1996 12:35:11 -0500 (EST) Hypercube, Inc. presents the First World HyperChem User Group Meeting September 8-11, 1996 Clevelands House, Minett, Muskoka Ontario, Canada First Announcement HyperChem is like any other powerful tool: the more you know about it, the more you get from working with it. For those who wish to learn more about working with HyperChem, the range of problems you can now tackle on a PC, and for those who wish to show other people how HyperChem can be used successfully in various fields of chemistry, Hypercube, Inc. (the developers of HyperChem) offer The First World HyperChem User Group Meeting. Objectives of the Meeting There are many of you who are doing a remarkable job with HyperChem in the research and teaching fields. Additionally, there are certainly even more uses that we are not aware of, as to how you are using HyperChem. With this in mind, we would like to bring all of you together so that we can share ideas and information. Experienced HyperChem users will be invited to provide introductory talks, and we, at Hypercube, will be there to present our views of how HyperChem can be used and our vision of future developments of HyperChem. We would like to hear your suggestions, since HyperChem is made for you, the end user. A small computer lab will be available, so that after the official hours of the Meeting, we can exchange ideas, demonstrate and learn the new uses and applications of HyperChem; or you can simply enjoy the beach, pools, tennis courts, or other facilities of this beautiful resort in the middle of Muskoka county and gorgeous Muskoka lake. Outline of the Meeting The Meeting will be divided in three sections depending on particular HyperChem (or other Hypercube products) uses in: (A) Research (B) Teaching (C) Association with other programs The first section (A), HyperChem in Research, will cover all the fields in chemistry and biochemistry where HyperChem can be used. The second section (B), HyperChem in Teaching, will cover all the teaching levels of chemistry where HyperChem is used. The third section (C), HyperChem in Association with other Programs, will cover all the possible uses of HyperChem in conjuction with other programs in the Windows environment (automation using scripts or Excel Macros, etc.) as well as the use of HyperChem in association with other molecular modeling or quantum chemistry programs. Costs and Venue In order to organize this Meeting and to bring experts talk about HyperChem, a small Registration fee of $100.00 US for academic, and $150.00 US for commercial users will apply. The Meeting will be held at Clevelands House, a beautiful resort on the Muskoka Lake just about 200 km north of Toronto. The resort has excellent conference facilities, as well as many recreational facilities, including four swimming pools, beach on the lake, tennis courts, water sports, facilities for children, etc. Accommodation The accommodation for all the participants of the Meeting will be at Clevelands House (Approximate prices including all the meals, taxes, and recreational facilities: Single: $195.00 CAN; Double: $145.00 CAN). Participants will be expected to make their own reservation directly with Clevelands House. Detailed instructions will follow in the Second Announcement on receipt of the attached form. Transportation Participants will be expected to make their own travel arrangements to Toronto International Airport. Shuttle Bus service will be available from the Airport to Clevelands House on both September 7th and 8th, as well as for the return to the Airport on September 11th and 12th. The Second Announcement will give complete details about the shuttle bus service, as well as the directions on how to reach Clevelands House if you are traveling by car. Preliminary Registration To tentatively register for the Meeting and to receive the Second Announcement, please complete the enclosed form and return as soon as possible (before April 1) to: Dr. Dragan Lj. Vuckovic Hypercube, Inc. Unit 7, 419 Phillip Street Waterloo, Ont. Canada N2L 3X2 e-mail: vuckovic@hyper.com Tel. (519) 725-4040 Fax: (519) 725-5193 The Second Announcement will be mailed in April Preliminary Registration Form The First World HyperChem User Group Meeting Clevelands House, Muskoka, ON, Canada September 8-11, 1996 Please send me the Second Announcement. NAME __________________________________________________ ORGANIZATION __________________________________________________ POSITION __________________________________________________ ADDRESS FOR CORRESPONDENCE __________________________________________________ __________________________________________________ ___________________________________________________ TEL. NO. __________________FAX NO._________________ I am interested in attending the Meeting ___, or attending the Meeting and presenting a paper ___, in section A, B or C (circle the appropriate section). SIGNATURE DATE _____________________________________________________ ___________________________________________________________________ Dr. Dragan Lj. Vuckovic phone: (519) 725-4040 International Marketing Manager fax: (519) 725-5193 Hypercube, Inc. e-mail: vuckovic@hyper.com 419 Phillip Street URL: http://www.hyper.com Waterloo, Ontario Canada, N2L 3X2 ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Jan 30 21:31:10 1996 Date: Tue, 30 Jan 96 17:20:57 -0500 From: polowin (Joel Polowin) To: "Thomas Futterer t4633" Subject: Re: HyperChem Release 4.5 for SGI Cc: hyperchem@hyper.com > From: "Thomas Futterer t4633" > Date: Tue, 30 Jan 1996 14:45:26 +0100 > > 1. Is it possible that HyperChem works in the background after I`ve > logged out from the system? Now it doesn`t. I do not know of any way of doing this. HyperChem always must display the workspace in a graphical window. That window can be redirected to another machine, which allows one to log off from the machine on which the HyperChem session was started, but if someone logs in on the machine that has the HyperChem window and then logs out, that stops HyperChem as well. If there was some way of redirecting the HyperChem display to some kind of "null display", the display equivalent of /dev/null , that would probably solve the problem. Unfortunately, we do not know of any way of doing that, and the people at SGI's technical support did not know of any way either. > 2. I have some ***.xyz files derived from x-ray studies. It is no > problem to open the file, but the atoms are not connected > automatically to get a molecule. Is there a way to this > automatically. If you save the structure in MOPAC Z-Matrix format and then read it back in, the input file filter will automatically generate bonds. You may need to edit them manually afterwards, since the algorithm that assigns bond orders does so on the basis of atom types and typical bond lengths. Real chemical structures often have bond lengths that are not "typical". 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 Jan 31 10:42:13 1996 From: "Roth W. ZFE BT MR 6" To: Hyperchem Subject: Graphite Date: Wed, 31 Jan 96 11:27:00 PST Hello, My name is Manfred Groeppel and I have a problem with my HyperChem version 4.0. I've got the PC-Version that runs at a pentium machine. I'm interested in the adsorption from alkanes onto the basal plane of graphite. The graphite was built as follows: Starting from benzene I added more and more phenyl rests and optimized the structure (962 atoms) with the mm+ force field. A second layer was copied and pasted in a distance from 3.35 A. After running a calculation by bringing an alkane close to the surface the optimized structure was saved. Re-opening the file brings the following buck. The distance between the two graphite layers is only 3.26A. This is very surprising as the graphite isn't activated during the optimization - so shouldn't be changed in any way. A second question is: When I optimize an alkane on the graphite surface and the graphite isn't activated. What kind of interactions are neglected? A last question: When I build the graphite via the Crystal builder from the Chem Plus module I obtain different "heats of adsorption" compared to the graphite build by the way it was described before. Why? Manny ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jan 31 17:03:21 1996 Date: Wed, 31 Jan 1996 08:46:39 -0800 To: hyperchem@hyper.com From: cbbrown@earthlink.net (Craig Brown) Subject: Leu zippers in the PDB. Hello Hyperchemers, I recently sent a message about modeling leucine zipper structures. Thank you very much for your feedback. I was told that there are leucine zipper, coiled-coil structures in the PDB. If anyone out there knows some or all of the file names to those zipper proteins, could you please fax or e-mail those names to me. Once again, forgive my questions and requests if they are either vague or too simple. I am very new to HyperChem. Thanks, Craig Brown Charles Drew University of Medicine and Science fax: (310) 533-0244 e-mail(s): cbrown@dhvx20.csudh.edu cbbrown@earthlink.net ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Jan 31 17:20:32 1996 Date: Wed, 31 Jan 96 12:37:36 -0500 From: polowin (Joel Polowin) To: "Roth W. ZFE BT MR 6" , Hyperchem Subject: Re: Graphite > From: "Roth W. ZFE BT MR 6" > Date: Wed, 31 Jan 96 11:27:00 PST > > My name is Manfred Groeppel and I have a problem with my HyperChem version > 4.0. I've got the PC-Version that runs at a pentium machine. I'm interested > in the adsorption from alkanes onto the basal plane of graphite. The > graphite was built as follows: > Starting from benzene I added more and more phenyl rests and optimized the > structure (962 atoms) with the mm+ force field. A second layer was copied > and pasted in a distance from 3.35 A. > After running a calculation by bringing an alkane close to the surface the > optimized structure was saved. Re-opening the file brings the following > buck. The distance between the two graphite layers is only 3.26A. This is > very surprising as the graphite isn't activated during the optimization - so > shouldn't be changed in any way. No, it shouldn't. Any optimization in which some atoms are selected should not move any atoms that are NOT selected, and I have never before had a report that they are moved. If you can send me a copy of the HIN file of the structure before optimization, I will try to reproduce the effect. How are you measuring the distance between the planes; how did you paste the second layer at a distance of 3.35 A? > When I optimize an alkane on the graphite surface and the graphite isn't > activated. What kind of interactions are neglected? All interactions that involve selected atoms will be included; only interactions that involve no selected atoms will be neglected. For the molecular mechanics calculations, only non-bonded interactions occur between molecules: electrostatic effects and van der Waals-type interactions. Unless you have added charges to the graphite atoms, only van der Waals- type interactions should be included. If you run an MM+ single-point calculation after setting the MechanicsPrintLevel in CHEM.INI to a value of 1 or greater, and starting a log file, you can get a complete list of all of the interactions included in the total. I think that MM+ will not give you a good model of this kind of adsorption since it does not include any of the pi interactions which are probably significant here. One of the semi-empirical methods would probably give more reasonable results. > When I build the graphite via the Crystal builder from the Chem Plus module > I obtain different "heats of adsorption" compared to the graphite build by > the way it was described before. Why? If the structures are the same, you should get the same results. How are you building the graphite with the Crystal Builder -- are you using it just to duplicate the layers, or to build one of the layers from smaller units? 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 Jan 31 19:30:20 1996 Date: Wed, 31 Jan 96 13:57:28 -0500 From: polowin (Joel Polowin) To: ico@siam.mi.cnr.it (Istituto di Chimica degli Ormoni), hyperchem@hyper.com Subject: Re: Chromium Parameters > Date: Fri, 26 Jan 1996 17:43:28 +0100 (MET) > From: ico@siam.mi.cnr.it (Istituto di Chimica degli Ormoni) > I am trying to minimize benzene chromium tricarbonyl (C6H6Cr(CO)3) without > success. > With MM and ZINDO the structure obtained are totally different from that one > determined with X-ray. I try to use ab initio minimization with my P-90 16 > Mb Ram but takes too long (more then one week). > Any suggestion how to modify the force field for MM? There is a place in > Internet where I can found such parameters? Modelling of transition metal complexes is a subject still requiring much development. ZINDO modelling of second-row transition metals is usually reasonably good but it often does not do well for first-row transition metals, especially carbonyls. My Ph.D. research was on modelling compounds, including derivatives of (C6H6)Cr(CO)3, with molecular mechanics. I found that if I did not try to bond the benzene ring directly to the Cr, but instead used structural restraints to fix the Cr--C distances to experimental values, other structural results and barriers to internal rotation were reasonably good. You might try asking in other forums such as the sci.chem Usenet group, or on the Computational Chemistry mailing list. To subscribe to the CCL, write to the list coordinator at CHEMISTRY-REQUEST@ccl.osc.edu . 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.