From chemistry-request@www.ccl.net Thu Feb 4 09:25:49 1999 From: Steven.Creve@dsm-group.com Date: Thu, 4 Feb 1999 15:22:07 +0100 Subject: CCL:pKa calculation To: CHEMISTRY@www.ccl.net Hi, could anyone point me to some good references (methods, applications, ...) for the a prioir calculation of pKa or pKb values? Thank you, Steven From chemistry-request@www.ccl.net Thu Feb 4 10:03:39 1999 From: "Stefan Fau" To: "CCL" Subject: RE: G:Freq in G94 Date: Thu, 4 Feb 1999 16:05:07 +0100 Dear Krys, the vibrational frequencies are derived from the force-constant matrix(second derivatives of the energy wrt. nuclear coordinates). In a non-linear molecule 6 of the 3*N_atoms degrees of freedom describe translation and rotation of the molecule. If there were no numerical inaccuracies and if the geometry was perfectly minimized, these 6 freqs would be zero since the SCF energy is independent of the orientation and location of the molecule. Because of the mentioned imperfections, three of the 6 "zero-freqs" are close to zero and the other three "zero-freqs" have low absolute values (typically in the range of 10 to 50 cm-1, depending on the quality of the geometry optimization). To avoid coupling, these "zero-freqs" are projected out and the remaining 3*N_atoms-6 x 3*N_atoms-6 matrix is diagonalized. For more details have a look into, e.g. "Introduction to Computational Chemistry" by Frank Jensen. It gives a good overview and is really affordable (~ DM 80). Stefan ___________________________________ Dr. Stefan Fau Fachbereich Chemie, AK Frenking Philipps-Universität Marburg 35032 Marburg, Germany fau@chemie.uni-marburg.de > I have question concerning log from IR calculation in G94. > Below is part of this log: > > Low frequencies --- -82.8125 -5.2461 -0.0021 0.0021 0.0064 7.1252 > > Low frequencies --- 10.1830 65.1288 69.2516 > > ****** 1 imaginary frequencies (negative signs) ****** > > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), > > Raman scattering activities (A**4/AMU), Raman depolarization ratios, > > reduced masses (AMU), force constants (mDyne/A) and normal coordinates: > > 1 2 3 > > A" A" A' > > Frequencies -- -82.7948 65.1108 69.2511 > > Red. masses -- 1.0165 1.0212 1.1460 > > First frequency is 1A"= -82.7948, and I can also see it in first line > that I gave: > "Low frequencies --- -82.8125" The second is 65.1108 cm^-1, so my > question what > are this "-5.2461 -0.0021 0.0021 0.0064 7.1252 10.1830" From chemistry-request@www.ccl.net Thu Feb 4 11:34:57 1999 From: "Stefan Fau" To: "CCL" Subject: Q:choosing "zero freqs" to be projected out Date: Thu, 4 Feb 1999 17:36:40 +0100 Dear CCLers, Gaussian (like many other programs) projects out the 6 "zero freqs" that belong to translation and rotation of a non-linear molecule before diagonalizing the remaining matrix. These "zero freqs" can be of similar magnitude as the lowest vibrational frequencies if the molecule is very floppy (I once had a molecule with 7 freqs of |ny|<15cm^-1). Does anybody know how the "zero freqs" are selected? Just by the absolute value of the raw frequency or is there some check for the type of movement (e.g. all atomic vectors of the mode parallel/orthogonal to the molecular translation/rotation vector) to avoid projecting out a vibrational frequency if vibrational and "zero" freqs are intermingled? I'll summarize if there is demand. Stefan ___________________________________ Dr. Stefan Fau Fachbereich Chemie, AK Frenking Philipps-Universität Marburg 35032 Marburg, Germany fau@chemie.uni-marburg.de From chemistry-request@www.ccl.net Fri Feb 5 15:00:54 1999 Received: from mail2.organik.uni-erlangen.de (lesath.organik.uni-erlangen.de [131.188.128.212]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA14386 Fri, 5 Feb 1999 15:00:52 -0500 (EST) Received: from wtewael.organik.uni-erlangen.de (wtewael [131.188.128.216]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id UAA01993 for ; Fri, 5 Feb 1999 20:57:30 +0100 (MET) Received: (from wdi@localhost) by wtewael.organik.uni-erlangen.de (8.8.7/8.1.59-FAU) id TAA06423 for chemistry@www.ccl.net; Fri, 5 Feb 1999 19:57:30 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9902052057.ZM6421@torvs.ccc.uni-erlangen.de> Date: Fri, 5 Feb 1999 20:57:29 +0000 In-Reply-To: Mark Forster "CCL:Drawing Lewis structures" (Feb 4, 11:45) References: <199902031541.JAA05098@hera.wku.edu> <36B98864.5DBE2B8C@nibsc.ac.uk> Reply-To: Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:Drawing Lewis structures Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Feb 4, 11:45, Mark Forster wrote: > Subject: CCL:Drawing Lewis structures > Dear Ron and Allen > > For a very inexpensive windows based package look at Molecules 3D from > molecular arts corporation. Some contact information on them follows. > Unfortunately their WWW page (http://www.molecules.com) does not seem > to be functioning. Yes, this package does have a Lewis structure drawing module. However, this company has a very dubious track record: a) They are the first chemistry software company I am aware of which was found guilty of email spamming by their ex-provider host4u.net (Host4u Abuse Team message dated 8 Sep 1998) after mass-mailing a typical spam mail (complete with their own private uncontrolled and unverifyable opt-out list and a reference to alleged compliance with federal bill 1619) advertising their 3D structure builder. b) They are selling for $199 apiece a 'Giant Library of 3D Molecular Models' and a 'Pharma CD'. These CDs are essentially unapproved copies of an old release of the NCI/NIH DTP structure database. The same structure data is freely available from various Internet sites (see for example http://www2.ccc.uni-erlangen.de/ncidb/, and the NCI DTP homepage http://dtp.nci.nih.gov/). They do not give (at least not on their Website) any credit for the origin of the data, or the coordinates of the structures (computed by the CORINA program, not their model builder) c) Compare that to their usage conditions of their WebMolecules(TM) online 3D structure display service usage conditions: This WebMolecules site contains copyrighted material, which is protected by US Federal Law and International Treaties. Unless you have our prior written agreement, all other uses, including but not limited to reverse engineering, repackaging, or any other reuse of the graphics, underlying data, or data manipulation source code is strictly prohibited. (The content of this service is not identical to the aforementioned data CDs, it contains only a few hundred structures) My personal opinion is that these business practices are deplorable and unethical. I would never consider to buy anything from a proven spammer. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566