From chemistry-request@server.ccl.net Thu Nov 25 06:27:17 1999 Received: from cmcind.far.ruu.nl (cmcind.pharm.uu.nl [131.211.56.43]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA04056 for ; Thu, 25 Nov 1999 06:27:16 -0500 Received: from pharm.uu.nl (fischer.far.ruu.nl [131.211.56.46]) by cmcind.far.ruu.nl (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id LAA07337; Thu, 25 Nov 1999 11:22:02 +0100 (MET) Sender: moret@pharm.uu.nl Message-ID: <383D0DC9.E21491FB@pharm.uu.nl> Date: Thu, 25 Nov 1999 11:22:01 +0100 From: "Ed E. Moret" Reply-To: E.E.Moret@pharm.uu.nl Organization: Utrecht University X-Mailer: Mozilla 4.61 [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: cis/trans rotation barrier in peptides? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL A question for the force field developers; I hope it is not a faq. It seems basic though. I would like to know what the experimental rotation barrier energy of the amide bond is in peptides of different composition? So, not just the readily accessible data on cis/trans isomerisation of prolines. If this is beyond measurement: has it been computed, taking into account solvation effects? With best regards Ed Moret -- | Ed E. Moret (@more@) Department of Medicinal Chemistry | Faculty of Pharmacy Utrecht University The Netherlands | Tel.: +31 30 2536979(2536958) Fax: +31 30 2536655 | E-mail: E.E.Moret@pharm.uu.nl WWW: http://wwwcmc.pharm.uu.nl/moret/ From chemistry-request@server.ccl.net Thu Nov 25 09:33:05 1999 Received: from mailhub.unibe.ch (mailhub.unibe.ch [130.92.254.109]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA05566 for ; Thu, 25 Nov 1999 09:33:04 -0500 Received: from ubecx01 (ubecx01.unibe.ch [130.92.6.40]) by mailhub.unibe.ch (PMDF V5.2-29 #33079) with ESMTP id <0FLR00L3F9B6T5@mailhub.unibe.ch> for chemistry@ccl.net; Thu, 25 Nov 1999 14:25:55 +0100 (MET) Received: from issi.unibe.ch (trace.unibe.ch [130.92.76.65]) by ubecx01.unibe.ch (PMDF V5.2-32 #33079) with ESMTP id <0FLR00CAS9E4AH@ubecx01.unibe.ch> for chemistry@ccl.net; Thu, 25 Nov 1999 14:27:40 +0100 (MET) Date: Thu, 25 Nov 1999 14:25:10 +0100 From: Stephan Graf Subject: CCL:frequencies vs. coordinates Sender: michael.graf-buhlmann@theol.unibe.ch To: chemistry@ccl.net Message-id: <383D38B6.3A58716D@issi.unibe.ch> MIME-version: 1.0 X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5 i686) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en References: <029301bf35d3$7a361700$b6d633d4@p.lodz.pl> Paneth wrote: > > > Dear all: > > I have a question regarding frequency calculations in G98. Depending on > > what's taken from the checkpoint, redundant internal or cartesian > > coordinates the normal vibrations are somewhat different. Unfortunately, > the > > isotopic differences are so large that the isotope effects are not > reliable. > > Below I give an abbreviated version - full output files are attached. > > my original posting turned out to be too large for automatic distribution so > the abovementioned files are zipped! > > > The question is which set should be trusted: > > > > 1st set: > > ..... > > #RHF 6-31++G** freq=(readisotopes,readfc) geom=check > > ---------------------------------------------------- > > 1/29=2,38=1/1; > > 2//2; > > 7/8=2,25=11/16; > > 99/5=2/99; > > ------------ > > comment line > > ------------ > > No Z-matrix found on checkpoint file. > > Cartesian coordinates read from the checkpoint file: > > ....... > > Frequencies -- 277.4024 357.4032 714.2104 > > > > 2nd set: > > ..... > > Redundant internal coordinates taken from checkpointfile: > > ............ > > Frequencies -- 278.9392 357.7119 701.2824 > > --------- > > Cheers, Piotr > > ****************************************************** > Professor Piotr Paneth > Department of Chemistry, Technical University > Zeromskiego 116, 90-924 Lodz, Poland > phone/fax: (+48 42) 631-3199 fax: (+48 42) 636-5008 > Hi, in your log files I've seen that the six low frequencies from the cartesian coordinates calculation are closer to zero than the values from the other calculation. As this frequencies represent translation and rotation they should be zero. Maybe one could take this values as a critera to compare both calculations. I find it also strange that in the calculation using internal coordinates all IR intensities are zero. Regards, Stephan -- Dr. Stephan Graf International Space Science Institute Hallerstrasse 6 Phone : ++41/31/631 32 54 CH-3012 Bern Fax : ++41/31/631 48 97 Switzerland email : stephan.graf@issi.unibe.ch From chemistry-request@server.ccl.net Thu Nov 25 14:47:35 1999 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA06763 for ; Thu, 25 Nov 1999 14:47:34 -0500 Received: from el1 ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with SMTP id <01JIR8TBUHK8004BFA@trentu.ca> for chemistry@ccl.net; Thu, 25 Nov 1999 13:41:56 EST Date: Thu, 25 Nov 1999 13:45:22 -0500 From: Errol Lewars Subject: Hypervalent molecules To: chemistry@ccl.net Message-id: <383D83C2.3802@trentu.ca> Organization: Trent University MIME-version: 1.0 X-Mailer: Mozilla 3.01Gold (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit 1999 Nov 25 Fernando Vila asked about refs to hypervalent molecules like NH4 (neutral, 9 electrons in the N valence shell). 15-20 years ago Professor Vedeen Smith of Queen's University, Kingston, Ontario, Canada [check out their Website]did calculations on on NH4, and maybe other hypervalents. It should be possible to find these refs with, e.g. Chem Abstr, and to use Chem Cit index to locate later ones to this kind of work. E. Lewars From chemistry-request@server.ccl.net Thu Nov 25 20:28:10 1999 Received: from ripspost.aist.go.jp (ripspost.aist.go.jp [150.29.9.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA07940 for ; Thu, 25 Nov 1999 20:28:09 -0500 Received: from ripspom.aist.go.jp (ripspom.aist.go.jp [150.29.45.1]) by ripspost.aist.go.jp (8.9.3/3.7W) with ESMTP id JAA17783 for ; Fri, 26 Nov 1999 09:22:40 +0900 (JST) Received: from tnhost.tniri.go.jp (tnhost.tniri.go.jp [150.82.48.1]) by ripspom.aist.go.jp (8.9.3/3.7W) with ESMTP id JAA28224 for ; Fri, 26 Nov 1999 09:22:39 +0900 (JST) Received: from tniri.go.jp (tnpc33.tniri.go.jp [150.82.49.136]) by tnhost.tniri.go.jp (8.8.7+2.7Wbeta7/3.6Wbeta7) with ESMTP id JAA21090 for ; Fri, 26 Nov 1999 09:20:31 +0900 (JST) Message-ID: <383DD70F.CF677C5@tniri.go.jp> Date: Fri, 26 Nov 1999 09:40:47 +0900 From: "Dr. Abhijit Chatterjee" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: COSMO Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Members, Few days before I posted a query about how to calculate the hydration energy by COSMO module of DMOL. I did not receive any response so far, so I am posting it again as a reminder for help. Abhijit chatt@tniri.go.jp