From dsmith@doane.edu Thu Feb 2 03:03:39 1995 From: dsmith@doane.edu Date: Thu, 2 Feb 1995 01:10:14 -0600 To: hyperchem@hyper.com Subject: sources of inorganic coordinates Hyperchemers: Is there a document (book, journal article, etc.) that is fairly available that has listings of the Cartesian coordinates (preferred) or crystalographic data for a number of *inorganic* compounds? We need this data to plug into a low-level modeling program on Macintosh that is compatable with Hypercard. This group ought to know where such data is. Thanks, Dave Smith Doane College Crete NE 68333-2496 (402)826-3585 dsmith@doane.edu ________________________________________________________________________ From polowin Thu Feb 2 13:11:43 1995 Date: Thu, 2 Feb 95 13:11:43 -0500 From: polowin (Joel Polowin) To: hyperchem Subject: Re: sources of inorganic coordinates > From dsmith@doane.edu Thu Feb 2 03:03:39 1995 [...] > Is there a document (book, journal article, etc.) that is fairly available > that has listings of the Cartesian coordinates (preferred) or crystalographic > data for a number of *inorganic* compounds? We need this data to plug into > a low-level modeling program on Macintosh that is compatable with Hypercard. > This group ought to know where such data is. Several of the journals carry such information regularly. _Journal of Inorganic Chemistry_ articles often include crystal data; _Organometallics_ does too. To say nothing of _Crsytallographica Acta_, if I've got the title right. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 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" to hyperchem-request@hyper.com ________________________________________________________________________ From Matthew.Harbowy@tjlus.sprint.com Fri Feb 3 11:53:04 1995 Date: Fri, 3 Feb 1995 09:35:00 -0500 From: Matthew.Harbowy@tjlus.sprint.com To: hyperchem@hyper.com Subject: ZINDO UV/Vis spectra The transition strength corresponds to the experimental measurement epsilon, the molar absorptivity coefficient such as represented in Beer's law. Naturally, the representation of the transition moment is that of the pure transition without the factor of (vibrational spreading?), which in some computation packages is represented by centering a gaussian on the transition moment. Because of the extreme degree of assumptions going into such a calculation, picturing the computed uv spectrum as one would a spectrophotometric observation seems silly at some level because there is low probability of any accuracy. For qualitative comparison, though, a decent oscillator strength on a particular transition might point to a proximate lambda-max of a spectrum. This would give some info on the transition, i.e. sigma->pi* or pi->pi* ad nauseam, and the molecular orbitals involved, akin to the older-style tables of approximate transitions for alkenes, carbonyls, etc. hope this is informative. matthew harbowy chemist, thomas j. lipton matthew.harbowy@tjlus.sprint.com ________________________________________________________________________ From 94970459@vax1.dcu.ie Fri Feb 3 14:08:17 1995 Date: Fri, 03 Feb 1995 17:53:15 +0000 (GMT) From: KANEPCHEM <94970459@vax1.dcu.ie> Subject: Cambridge Structural Database To: hyperchem@hyper.com Hi, Do you know if data on organic molecules from the Cambridge Structural Database is in the CSD file format so that I can generate 3-d pictures of such molecules with the ChemPlus software. Regards, Paddy Kane ________________________________________________________________________ From JSL@mmf.ruc.dk Wed Feb 8 07:04:31 1995 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: hyperchem@HYPER.COM Date: Wed, 8 Feb 1995 12:20:17 +0100 Subject: Oscillator Strengths and ZINDO/S OSCILLATOR STRENGTHS The oscillator strength f of a spectroscopic, dipole-induced transition is a measure of the transition probability and is a dimensionless quantity. Experimentally, the oscillator strength of an electronic transition may be determined as ( f = 4.319E-9 | Eps(nu) dnu ) band where Eps(nu) is the molar absorbance (L/(mol cm)) as a function of wavenumber nu (1/cm). The integral is over the whole wavenumber range of the absorption band corresponding to the electronic transition, incl. vibronic components. The oscillator strength f is thus proportional to the AREA under the absorption curve and depends on the "intensity" as well as the shape of the band. Theoretically, the oscillator strength of an electronic transition is related to the transition energy and the transition moment, f = const. (E2 - E1) |M|**2 where E2 - E1 is the transition energy and |M|**2 is the square of the length of the transition dipole moment vector M (these quantities are computed by ZINDO/S and are obtainable via the HyperChem logfile). If |M| equals zero for reasons of symmetry, the transition is said to be symmetry forbidden. The direction of the molecular vector M is referred to as the polarization of the transition, and can frequently be determined experimentally. For further information, see f.ex. the volume by Erik W. Thulstrup and Josef Michl: "Elementary Polarization Spectroscopy", Verlag Chemie (VCH) 1989. Yours sincerely, Jens Spanget-Larsen _________________________________ _________________________________ | | | | Jens Spanget-Larsen | Phone: +45 46757711 | | Associate Professor, dr.scient. | - direct: +45 46757781 * 2710 | | Department of Chemistry (17.2) | - private: +45 42840320 | | Roskilde University | Fax: +45 46757721 [Dept.] | | RUC, P.O. Box 260 | - +45 46757401 [RUC] | | DK-4000 Roskilde, Denmark | Internet: JSL@mmf.ruc.dk | |_________________________________|_________________________________| ________________________________________________________________________ From chjp@convex.uovs.ac.za Tue Feb 14 07:03:35 1995 Date: Tue, 14 Feb 95 10:22:24 +0100 From: chjp@convex.uovs.ac.za (JP Steynberg) To: hyperchem@HYPER.COM Subject: Default parameters I would appreciate any information on how to find out for which bends in a molecule default parameters are being used when the message "Default parameters being used for bends" appears in the *.log file. It can be done by checking the mmpben.txt file but isn`t there some way of doing it with HYPERCHEM? Regards, JP Steynberg email: chjp@convex.uovs.ac.za ________________________________________________________________________ From polowin Tue Feb 14 10:47:34 1995 Date: Tue, 14 Feb 95 10:47:34 -0500 From: polowin (Joel Polowin) To: hyperchem Subject: Re: Default parameters > From chjp@convex.uovs.ac.za Tue Feb 14 07:03:35 1995 > Date: Tue, 14 Feb 95 10:22:24 +0100 > From: chjp@convex.uovs.ac.za (JP Steynberg) > To: hyperchem@HYPER.COM > Subject: Default parameters > > I would appreciate any information on how to find out for which bends in a > molecule default parameters are being used when the message "Default > parameters being used for bends" appears in the *.log file. It can be > done by checking the mmpben.txt > file but isn`t there some way of doing it with HYPERCHEM? If you set MechanicsPrintLevel, in CHEM.INI, to 6 or higher, start a log file, and do a single-point MM+ calculation, the log will begin with a complete list of the atoms and interactions for which default parameters are used. The other force fields behave somewhat less gracefully when faced with unknown parameters, and less information is available from the log file. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 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" to hyperchem-request@hyper.com ________________________________________________________________________ From 94970459@vax1.dcu.ie Sat Feb 18 12:03:52 1995 Date: Sat, 18 Feb 1995 16:34:21 +0000 (GMT) From: KANEPCHEM <94970459@vax1.dcu.ie> Subject: Ionic Radii To: hyperchem@hyper.com How can I set the radius of sodium+ ion, when using the MM+ force field. I'm sure it has something to do with modifying the MM+ parameter set, but what exactly do I do ? Thanks in advance for any assistance. Regards, Paddy Kane Dublin City University Ireland ________________________________________________________________________ From Howard.Shertzer@UC.Edu Tue Feb 21 00:09:53 1995 From: Howard.Shertzer@UC.Edu Date: Mon, 20 Feb 1995 21:14:03 -0500 (EST) Subject: text To: hyperchem@hyper.COM Can anyone suggest a good introductory text on molecular modeling, suitable for upperclass undergraduates or first-second year graduate students in toxicology. These students do not usually have an extensive mathematics background and their interests are in the application to compounds of environmental and toxicological concern. The texts I've seen are too math-oriented. I am hoping for something to supplement the Hyperchem user manual. ________________________________________________________________________ From S0683398@DOMINIC.BARRY.EDU Tue Feb 21 17:06:54 1995 From: S0683398@DOMINIC.BARRY.EDU Date: Tue, 21 Feb 1995 16:05:10 -0500 (EST) Subject: new force field To: hyperchem@hyper.com Hello, We are trying to compile a new mm+ force field for gadolinium complexes. We have the data in *str.txt *tor.txt etc. files but HyperChem does not recognise them in the "Choose Parameter Set" menu. I thought I adapted the chem.ini file correctly, however it is still not being recognised. So far we have adapted the chem.rul, and the chem.ini, as well as written the following new files: *ben.txt *str.txt *tor.txt *poop.txt but are unable to compile a PAR file. We would appreciate any advise from those who have successfully created force fields themselves! Sincerely, Carrie Kontogiannis ________________________________________________________________________ From GF@chemie.uni-paderborn.de Thu Feb 23 08:04:41 1995 From: "Gregor Fels" To: hyperchem@hyper.com Date: Thu, 23 Feb 1995 12:26:42 GST Subject: free electrons of C=O group Dear HyperChem users when a C=O group containing compound is geometrically optimized in HyperChem (using e.g. MM+ or AM1) the free electron pairs of the carbonyl-oxygen (sp2-hybridization) come out completely sticking out of the C=O plain (torsion angles of around 30-50 degree for C-C-O-electron pair. The angle between the two electron pairs always is around 105 degree. I expected the electron pairs to lay within the C=O plain. Can somebody please comment on this stange behavior? Gregor Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 05251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de ________________________________________________________________________ From Matthew.Harbowy@tjlus.sprint.com Thu Feb 23 13:10:17 1995 From: Matthew.Harbowy@tjlus.sprint.com To: chemie.uni-paderborn.de!GF, hyperchem@HYPER.COM Subject: Re: free electrons of C=O group The electron pairs are meaningless in an AM1 calculation, so minimization using semiempirical techniques of the so-called electron pair groups is not 'realistic'. The electron pairs are really just pseudo-reference points for hydrogen bond contributions and the like, so I don't believe they're intended to be 'physical' and you probably should ignore their behavior. matt harbowy thomas j. lipton ______________________________ Reply Separator _________________________________ Subject: free electrons of C=O group Author: chemie.uni-paderborn.de!GF@hyper.hyper.com at INTERNET Date: 02/23/95 9:08 AM Dear HyperChem users when a C=O group containing compound is geometrically optimized in HyperChem (using e.g. MM+ or AM1) the free electron pairs of the carbonyl-oxygen (sp2-hybridization) come out completely sticking out of the C=O plain (torsion angles of around 30-50 degree for C-C-O-electron pair. The angle between the two electron pairs always is around 105 degree. I expected the electron pairs to lay within the C=O plain . Can somebody please comment on this stange behavior? Gregor Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 05251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de ________________________________________________________________________ From polowin Sun Feb 26 17:51:58 1995 Date: Sun, 26 Feb 95 17:51:58 -0500 From: polowin (Joel Polowin) To: hyperchem Subject: Re: How to get help... > Date: Sun, 26 Feb 1995 08:59:01 +0001 (EST) > From: William Leigh > Subject: How to get help with problems with HyperChem & HyperNMR > > I have just installed Hyperchem, ChemPlus, and HyperNMR and am > experiencing problems. How do I get help? By phoning the company, or sending E-mail to 'support@hyper.com' or to me at 'polowin@hyper.com'. What's up? Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 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" to hyperchem-request@hyper.com ________________________________________________________________________ From M.Duhm@uea.ac.uk Mon Feb 27 07:03:47 1995 Date: Mon, 27 Feb 1995 10:51:07 +0000 (GMT) From: Mark Duhm Subject: To: hyperchem I am currently undertaking my 3rd yearresearch project at UEA. For my project, I am trying to use Hyperchem to model Phthalocyanine and related compounds using Bio+ - I am using the Bio83 parameters. My problem is that phthalocyanine is a planar molecule, but Hyperchem keeps bending it whenever I geometry optimise. Has anyone encountered this before, and if so could you tell me - 1)Am I doing something wrong 2)Any parameters that I might need to make the molecule planar. Mark. ________________________________________________________________________ From polowin Tue Feb 28 13:52:40 1995 Date: Tue, 28 Feb 95 13:52:40 -0500 From: polowin (Joel Polowin) To: hyperchem Subject: Phthalocyanines > Date: Mon, 27 Feb 1995 10:51:07 +0000 (GMT) > From: Mark Duhm > Subject: > > I am currently undertaking my 3rd yearresearch project at UEA. For my > project, I am trying to use Hyperchem to model Phthalocyanine and related > compounds using Bio+ - I am using the Bio83 parameters. My problem is > that phthalocyanine is a planar molecule, but Hyperchem keeps bending it > whenever I geometry optimise. Has anyone encountered this before, and if > so could you tell me - > 1)Am I doing something wrong > 2)Any parameters that I might need to make the molecule planar. I've been trying to model phthalocyanine with bio+ and can't get it to work with the default parameter sets at all -- it keeps warning of missing parameters. The model builder doesn't give planar structures for phthalocyanine nor its metal-centred derivatives. If there's a metal coordinated to the four central nitrogen atoms, you can add two lone pairs to the metal, one above and one below the ring; the model builder then makes the structure planar. If the structure is drawn with delocalized bonds instead of single and double bonds, the model builder again makes planar structures for phthalocyanine or for derivatives with 4-coordinated metal atoms when those atoms also have lone pairs attached. Minimizing with the MM+ force field gives planar results. You can force the geometry to be planar by adding restraints. If you specify that the torsion angles N1-N2-N3-N4, N2-N3-N4-N1, N3-N4-N1-N2, AND N4-N1-N2-N3 (for the four central N atoms, numbered in a circle) should be 0' with a large force constant, the system will stay planar. (Note that if system energy is important to you, after structural optimization you should remove the restraints and calculate the single- point energy of the system, to obtain a value without the contribution of the restraint factors.) Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 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" to hyperchem-request@hyper.com ________________________________________________________________________ From polowin Tue Feb 28 15:43:36 1995 Date: Tue, 28 Feb 95 15:43:36 -0500 From: polowin (Joel Polowin) To: hyperchem Subject: Re: lone pairs of sp2 oxygen > From: "Gregor Fels" > Date: Tue, 28 Feb 1995 17:06:19 GST > Subject: lone pairs of sp2 oxygen > > When I optimize acetone including the lone pairs of oxygen (by > either method MM+ and AM1 respectively) the geometry of the system > comes out fine. But this is about the only compound that works well. > Everything is different when you try to calculate e.g. acetaldehyde. I don't even get acetone to come out with the "correct" orientations of the lone pairs. The thing is that the "lone pairs" aren't real atoms like the rest; they're convenient to add in, sometimes, as visualization aids or to help the software to identify a certain type or category of atom. There are a few cases in which they're needed in calculations; they can help a square-planar system to stay planar, for example. But for most purposes, you don't need them. When you draw acetone or acetaldehyde, and have HyperChem determine the atom types, it comes up with the same results whether you add the lone pairs or not. The AM1 energy calculation for acetone gives the same energy whether the lone pairs are present or not; it completely ignores them. MM+ does include an energy contribution from them, since there are parameters in the files for them. The MM+ atom type for the carbonyl oxygen is O1; lone pairs are type LP. There are no parameters in any of the MMP files that involve an O1 bonded to an LP atom; it ends up using default parameters, which tell it that the four groups attached to two sp2 atoms should all be coplanar, and that all of the angles C-O-LP and LP-O-LP should be 104.51'. (Set MechanicsPrintLevel=6 in CHEM.INI before starting HyperChem; optimize acetone; start logging calculations; do a single- point energy calculation; stop logging.) The compromise that results from all of these conditions, plus the non-bonded interactions, is the somewhat strange positioning of the lone pairs that you see. If you modify the parameters to specify that the LP-O1-LP angle shouldn't have an energy factor (define an LP-O1-LP parameter with a force constant of 0), the bending becomes much less pronounced, and the two lone pairs are then stable on opposite sides of the molecular plane. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 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" to hyperchem-request@hyper.com