From chemistry-request@ccl.net Thu Jul 30 01:05:51 1992 Date: Wed, 29 Jul 92 16:12:56 EDT From: doug@star2.cm.utexas.edu (William D Clendening) To: chemistry@ccl.net Subject: AVS chemistry viewer Status: R Hello, We are looking into buying the AVS Chemistry Viewer and would appreciate any comments from people who are familar w/ this product. Thanks, doug clendening doug@star2.cm.utexas.edu --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Jul 30 01:45:30 1992 Date: Wed, 29 Jul 1992 18:30 CST From: "JORGE M. SEMINARIO" Subject: Re: DFT calculation and ab initio To: zheng@violet.berkeley.edu Status: R > I am doing a calculation using the DFT program such as Dmol and the SCF total >energy is very different from what I got using G90 at similar basis set. What >is the relationship between these two total energies? Should not they be the > same 9in principle)? Any help will be appreciated. >Yajun Zheng Dear Yajun, In principle, if you use the same basis set and do a full ci in ab initio and a DFT using a correct functional, you will have the same energy for both theories. This is, of course, ignoring technicalities in the programs like the use of basis set for the density and for the wave functions. In practice, you are probably not using a full ci in ab initio neither the correct functional in DFT but approximations in both cases. If you used a HF method in ab initio, portion of the electron-electron exact operator was not considered in the hamiltonian (giving raise to an error, the so called correlation energy). On the other hand, The exchange-correlation (where the correlation portion is not the HF correlation of above) functional in DMol is a local one, which is a truncation of what is supposed to be the exact functional (sort of gradients expansion). Ab initio methods are exact for one electron systems. From where, approximations are extended to many electrons by different procedures: HF, MP, CI, etc. However, DFT methods start at the other end; the solutions for an infinite uniform electron system can be know as precisely as we want although in close form only for very special cases. From these exact solutions approximations are made in order to solve more realistic cases (non uniformity of the density) usually using density gradients in the exchange-correlation functional. Since the two approximations start at opposite ends, they necessarily do not have to coincide on their total energies of their low order approximations. Jorge M. Seminario jsmcm@uno.edu --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From FRENKING@DMRHRZ11.bitnet Thu Jul 30 06:34:18 1992 Date: Thu, 30 Jul 92 12:34:12 CET To: chemistry-request@ccl.net From: FRENKING%DMRHRZ11.BITNET@vm.gmd.de Status: R Dear fellow netters, I am running CI(SD) calculations using G90, and I am trying to extract the coefficient of the HF configuration. The manual says (page 165) that "Norm(A1) - 1 gives a measure of the correlation correction to the wavefunction." But what exactly is the coefficient for the HF configuration? My guess is that it is given by 1/Norm(A1), but I am not sure. Any comments? Thank you, Gernot Frenking frenking@dmrhrz11.bitnet From chemistry-request@ccl.net Thu Jul 30 08:23:10 1992 Date: Thu, 30 Jul 92 19:27:16 +1000 From: mgw@stan.xx.swin.OZ.AU (Margaret Wong) To: chemistry@ccl.net Subject: NMR processing packages Status: R Dear Netters We are currently looking for NMR programs to process our data off-line. We would be very interested to hear your opinions on any programable to work on a unix- workstation, PC or MAC. We need to be able to process 2-D data. We are also interested in programs which handle relaxation curve fitting preferably as part of the NMR processing package. Thanks Margaret Wong (mgw@stan.xx.swin.oz.au) --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Jul 30 12:11:55 1992 Date: 30 Jul 1992 09:30:19 -0400 (EDT) From: GRADR@ACFcluster.NYU.EDU Subject: Macromodel To: CHEMISTRY@ccl.net Status: R I am working on minimizing Acetyl Amino Florene (AAF) using MM2. The force field parameters for the Nitrogen ( atom type N3 ) bound to a C2 carbon and a carboxyl group is not found in the parameter file MM2.FLD. If anybody has this information or a suggestion about getting it please send E-mail to "gradr@acf7.nyu.edu" Thanks in advance for your help. Rosalyn Grad --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Jul 30 12:35:56 1992 Date: Thu, 30 Jul 92 09:19:42 EDT From: Mingzuo Shen To: chemistry@ccl.net Subject: dmol energy gradients problem Status: R Hi all, zheng@violet.berkeley.edu was wondering why the total energy from dmol was different from the total energy from Gaussian-xx. They should be different in principle. I had a chance to run dmol, available from the IBM 3090 (AIX/370) at the Cornell Theory Center. I run NH3 using Cs symmetry (because dmol at present only knows about D2h and its subgroups). While the input geometry has C3v symmetry intrinsically, I got a set of energy gradients which is not C3v. In other words, if I let dmol optimize NH3 without intervection, I would get something which has two different N--H bond lengths. What should be done to ensure that NH3 stays in C3v even when nominally we use Cs in dmol. Thanks for any suggestion. Here is the output of a GRADIENT calculation: df ATOMIC COORDINATES DERIVATIVES df x y z x y z df N 0.000000 0.000000 0.000000 -0.000320 -0.031873 0.000000 df H 1.777400 -0.804967 0.000000 0.008222 0.010543 0.000000 df H -0.888700 -0.804967 1.539274 -0.004082 0.010685 0.007064 df H -0.888700 -0.804967 -1.539274 -0.004082 0.010685 -0.007064 Note that even though the y-coordinates of the three hydrogens are the same, the y-components of the gradients are not the same. This result was obtained using the XFINE mesh grid in numerical integration. Mingzuo Shen P.S. NH3 may not be very bad. The problem arises when I try to use dmol to optimize a real molecule such as Co4(CO)12 in C3v. --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Jul 30 14:41:58 1992 Date: Thu, 30 Jul 92 09:33 CDT From: CUNDARIT%MEMSTVX1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: MG analogues of TM and Ln reactions To: chemistry@ccl.net Status: R Hi, Does anyone have a handy compendium of what must be the enormous literature of molecular hydrogen reactivity? Currently, we are studying transition metal and lanthanide catalyzed H/D exchange and are interested in comparing our results with activation energies and TS geometries for well known main-group analogues, calculated at high levels of theory. Reactions of interest are: a) atom/diatom reactions. H + H2 ---> H2 + H (also hydride, proton, and deuterated analogues) b) degenerate sigma-bond metathesis reactions. X-H + H2 ---> HX + H2 (X = H, Li, CH3, NH2, OH, F, SiH3, etc.) Tom Cundari Assistant Professor Department of Chemistry Memphis State University Memphis, TN 38152 phone:901-MSU-2629 fax:901-MSU-EIGS e-mail:cundarit@memstvx1.memst.edu --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Jul 30 18:34:30 1992 Date: Thu, 30 Jul 1992 16:20 EST From: J_BROWN@uvmvax.uvm.edu Subject: NMR software To: chemistry@ccl.net Status: R Margaret Wong (mgw@stan.xx swin.ox.au): There are many NMR simulation programs that are availible through QCPE (Quantum Chemistry Program Exchange) at Indiana University (Contact Richard Counts at bitnet countsr@iubacs or phone (812) 855-4784). Our group uses a modified version of DNMR (QCPE # 466) and UEANMR (QCPE #188). These programs simulate 1D spectra. --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Jul 30 19:32:25 1992 Date: Fri, 5 Jun 92 14:37:00 PDT From: rak@igor.caltech.edu (Robert A. Kumpf) Subject: Phone Number for QCPE? To: chemistry@ccl.net Status: R Hi, Does anyone have the current phone number for QCPE? The number I have ( (812) 335-4784 ) is no longer in service. Thanks, Bob Kumpf Email: rak@igor.caltech.edu --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Jul 30 20:50:45 1992 Date: Thu, 30 Jul 92 16:19:46 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) To: CHEMISTRY@ccl.net Subject: Natural Populations in G90 Status: R Is there a keyword in GAUSSIAN-90 that will do natural population analyis? I know that it can be done by explicitly stating the non-standard route, but this is such a pain. Also, does anyone have an explanation for the following warning I obtained in an NPA run of CO at 6-311+G*(6D): WARNING: Population inversion found on atom C 1 Population inversion found on atom O 2 Thanks! Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 smb@smb.chem.niu.edu --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Jul 30 21:45:18 1992 Date: Thu, 30 Jul 1992 17:22:54 EDT From: JOHNSON@CMCHEM.CHEM.CMU.EDU (Benny Johnson) Subject: Summary of responses to small-molecule experimental data question To: chemistry@ccl.net Status: R Thanks to all who responded to the query below. Here is a summary of the responses. Benny Johnson Carnegie Mellon University ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Can anyone give me references which collect together reliable, up-to-date experimental values of various molecular properties -- geometries, dipole moments, vibrational frequencies? I'm interested in these values mainly for small neutral systems with first-row atoms. ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- From: Chris D Paulse Try the Landoldt Bornstein tables of spectroscopic data for molecules. THey have at least two volumes on molecular structure of gas phase polyatomic molecules, and another volume devoted to molecular properties (dipole moments, quadrupole coupling constants, magnetic g factors, etc.) all obtained from gas phase measurements such as microwave spectroscopy. As for vibrational frequencies, theres no real definitive collection. Try a search in the Journal of Physical and Chemical Reference Data. Shimanouchi is an author you should look for. Whenever you see a structure in the Landolt Bornstein tables as r_z, that means someone has empirically derived a force field for the molecule. Good Luck, Chris Paulse ---------------------------------------------------------------------------- From: bbesler@ouchem.chem.oakland.edu (Brent H. Besler) Well the 1992-1993 Handbook of Chemistry and Physics has just been released. Unfortunately there is not that much as far as geometries are concerned, but dipole moments, heats of formation, EA's, and IP's are there. Jim Stewart's March 1990 issue of the Journal of Computer Aided Molecular Design compilers alot of small molecule data that was used in parameterizing the MNDO-PM3 semiempirical method. ---------------------------------------------------------------------------- From: Kurt.Hillig@um.cc.umich.edu WRT your question on small-molecule structure/dipole/vibration info - Prof. Barbara Stark and coworkers at the University of Ulm (Germany) havs for many years been abstracting the microwave/IR spectroscopy literature and distributing a bibliography. All small molecules, mostly neutrals, lots of gas-phase structure and dipole information and some vibrational info as well. I don't know how many people in the US subscribe, but I know that Bob Kuczkowski her at Michigan does. (From Bob Kuczkowski:) Write to: Dr. Jurgen Vogt Documentation center U. of Ulm Ulm, Germany. ---------------------------------------------------------------------------- --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Thu Jul 30 23:14:27 1992 To: chemistry@ccl.net Subject: Re: NMR software Date: Thu, 30 Jul 92 20:06:06 -0400 From: radomski@mond1.ccrc.uga.edu Status: R J_BROWN@uvmvax.uvm.edu wrote: >There are many NMR simulation programs that are >availible through QCPE (Quantum Chemistry Program Exchange) >at Indiana University (Contact Richard Counts at bitnet >countsr@iubacs or phone (812) 855-4784). Our group uses a >modified version of DNMR (QCPE # 466) and UEANMR (QCPE #188). >These programs simulate 1D spectra. Besides these, there is quite good (and unexpensive, singe license costs about $200) package sold by Hare Research Inc. 14810 216th Avenue NE, Woodinville, WA 98072, USA. They call it "Felix", and it is currently into ver 2.5. Both 1D and 2D modes are supported. It runs under Unix on SUNs and SGIs (promissed version for RISC DECstations under X failed to emerge so far), and which might be of some iterest - the same interface is implemented in the version running on PC under DOS (it is quick enough for uncomplicated 1D stuff; I know also about availability of the Windows version, but can't say how good it might be). Regards, Jan P. Radomski Complex Carbohydrate Research Center, University of Georgia, 220 Riverbend Rd., Athens, 30602 GA. Ph. (706) 542-4452 Fax (706) 542-4412 e-mail: radomski@mond1.ccrc.uga.edu --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net ---