From owner-chemistry@ccl.net Mon May 19 00:29:01 2008 From: "Inbal Tuvi-Arad inbaltu-#-openu.ac.il" To: CCL Subject: CCL:G: IRC and decimal digits Message-Id: <-36994-080519002735-32041-02uYUYMEdxl9IV8LaaCfyw a server.ccl.net> X-Original-From: "Inbal Tuvi-Arad" Date: Mon, 19 May 2008 00:27:32 -0400 Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu++openu.ac.il] Hello CCL subscribers I have a question regarding IRC calculations in Gaussian 03, and I hope you can help me. I'm doing IRC calculations on isomerization reactions of small molecules. I usually go far beyond 6 points in both directions in order to explore the complete reaction path. Sometimes, the calculations stops before the final point with an error message. In this case, the results file does not include the summary table with the energy, coordinates and IRC value. I would like to be able to extract the relevant information from the file up to the failure point as I need it for further calcaultions outside Gaussian. However, it seems that the accuracy of the data is different in the text before the summary table as compared to the one in the table. Specifically, in the summary table, the Cartesian coordinates are given with 5 decimal digits, while in the text prior to the table they are given in 4 decimal digits. Where does Gaussian take the data of the final table then? Is it coming from the Checkpoint file? I also tried to extract the data using Molden - in which case I got the coordinates with 6 digits. How can that be? Does this means the 6th digit is meaningless? What about the 5th one? Here is a sample of the final output of one point on the reaction path followed by the relevant lines of the summary table. **************************************************************************** -- Optimized point # 21 Found. ---------------------------- ! Optimized Parameters ! ! (Angstroms and Degrees) ! ---------------------- ---------------------- ! Name Value Derivative information (Atomic Units) ! ------------------------------------------------------------------------ ! X1 -0.0503 -DE/DX = -0.0029 ! ! Y1 -0.0008 -DE/DX = 0.0029 ! ! Z1 0.0001 -DE/DX = 0.0 ! ! X2 0.9885 -DE/DX = -0.0004 ! ! Y2 -0.0521 -DE/DX = -0.002 ! ! Z2 -0.0007 -DE/DX = 0.0 ! ! X3 -0.3155 -DE/DX = 0.0036 ! ! Y3 1.2164 -DE/DX = 0.0047 ! ! Z3 0.0 -DE/DX = 0.0 ! ! X4 -1.3495 -DE/DX = -0.0004 ! ! Y4 1.3284 -DE/DX = -0.0056 ! ! Z4 0.0009 -DE/DX = 0.0 ! ------------------------------------------------------------------------ RADIUS OF CURVATURE = 0.83355 NET REACTION COORDINATE UP TO THIS POINT = 2.09840 # OF POINTS ALONG THE PATH = 21 # OF STEPS = 2 Calculating another point on the path **************************************************************************** The same point on the summary table looks like this: **************************************************************************** ---------------------------------------------------------------------- Summary of reaction path following: (Int. Coord: Angstroms, and Degrees) ---------------------------------------------------------------------- ENERGY RX.COORD X1 Y1 Z1 1 -110.63715 -2.09840 -0.05026 -0.00081 0.00008 .. X2 Y2 Z2 X3 Y3 1 0.98848 -0.05210 -0.00075 -0.31546 1.21640 .. Z3 X4 Y4 Z4 1 0.00000 -1.34948 1.32840 0.00087 **************************************************************************************************************** Any idea will be most appreciated. Sincerely, Inbal __________________________________________ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel 108 Ravutski St. POB 808 Raanana 43107 Israel Tel: 972-9-778-1773 Fax: 972-9-778-0661 Email: inbaltu[a]openu.ac.il __________________________________________ From owner-chemistry@ccl.net Mon May 19 11:28:01 2008 From: "Prabha Lakshmi prabhalak26() yahoo.co.in" To: CCL Subject: CCL: list of isosters/bioisosters Message-Id: <-36995-080519061526-19256-D7zuo+GS+2jQeIZKLozYSQ*server.ccl.net> X-Original-From: Prabha Lakshmi Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Mon, 19 May 2008 15:45:11 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Prabha Lakshmi [prabhalak26|a|yahoo.co.in] Dear Sir,=0Aany suggestion to find a list/table of chemical substituents fo= r isosteric/bioisosteric replacement?=0AThank you all.=0APrabhalak=0A=0A=0A= Best Jokes, Best Friends, Best Food and more. Go to http://in.promos.= yahoo.com/groups/bestofyahoo/ From owner-chemistry@ccl.net Mon May 19 13:33:00 2008 From: "Andrew Fant fant[A]moleculargeek.com" To: CCL Subject: CCL: list of isosters/bioisosters Message-Id: <-36996-080519125117-17210-pNyWC1sW9ima8J8Rp2H0kQ(a)server.ccl.net> X-Original-From: Andrew Fant Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 19 May 2008 12:11:21 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew Fant [fant~~moleculargeek.com] Prabha Lakshmi prabhalak26() yahoo.co.in wrote: > Sent to CCL by: Prabha Lakshmi [prabhalak26|a|yahoo.co.in] > Dear Sir, > any suggestion to find a list/table of chemical substituents for isosteric/bioisosteric replacement? > Thank you all. > Prabhalak Prabhalak, Almost any medicinal chemistry text will have tables with some examples to get you started. I'd recommend Patrick, personally. There was also a review in Acc.Chem.Res. a few years back that I can't lay my hands on at the moment. Obviously, a complete list is not possible, but there are enough examples in those references to get you started and thinking about proposing new ones. Andy