From owner-chemistry@ccl.net Thu Jun 4 00:03:00 2009 From: "D. Boyd dboyd{:}iupui.edu" To: CCL Subject: CCL: QCPE Message-Id: <-39433-090603120321-7292-P3Weoib9jiqDrfB0LsGP+g|server.ccl.net> X-Original-From: "D. Boyd" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Wed, 3 Jun 2009 11:26:20 -0400 Mime-Version: 1.0 (Apple Message framework v930.3) Sent to CCL by: "D. Boyd" [dboyd_+_iupui.edu] Hola, After Mr. Richard Counts retired from managing QCPE, the famous crystallographer Professor John C. Huffman of Indiana University took over responsibility for it. However, he too has now retired. I am not aware of what has happened to the many programs in the QCPE. Presumably they are residing on some storage device at Indiana University, Bloomington. Dr. Huffman's email address is huffman-$-indiana.edu . Good Luck. A brief tribute to and history of QCPE can be found in the Preface of: Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 2000, Vol. 15, pp. v-xxxv. Don Boyd From owner-chemistry@ccl.net Thu Jun 4 08:45:01 2009 From: "Minho Kim astro33=ajou.ac.kr" To: CCL Subject: CCL: please help me. Message-Id: <-39434-090602213521-18032-NTUNpc5PjXoJlHlL7cdmaA=server.ccl.net> X-Original-From: "Minho Kim" Date: Tue, 2 Jun 2009 21:35:17 -0400 Sent to CCL by: "Minho Kim" [astro33-#-ajou.ac.kr] Hello! I calculated ground state of phenol using HF & MP2 method. HF method calculated well, but MP2 has a big problem. Freq. Calc. result has an imagenary number, so vibration frequency has minus value. I calculated several geometry of phenol, but they converged same result. why did't MP2 method calculate well? How can I do? Sorry, my English is very poor. Thank you for read. ----------------------------------------------- You can get LOG file. http://astrostars.v3webhard.com/chemical/phenol_opt7.log From owner-chemistry@ccl.net Thu Jun 4 13:38:01 2009 From: "Johnson III, Russell D. Dr. russell.johnson : nist.gov" To: CCL Subject: CCL: non-planar phenol Message-Id: <-39435-090604110855-26869-hdmZkoUux/sNt3uqlXp7mw^server.ccl.net> X-Original-From: "Johnson III, Russell D. Dr." Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Thu, 4 Jun 2009 10:37:46 -0400 MIME-Version: 1.0 Sent to CCL by: "Johnson III, Russell D. Dr." [russell.johnson^nist.gov] This may be another example of MP2 and certain basis sets yielding non-plan= ar structures for arenes. For example see: "Popular Theoretical Methods Predict Benzene and Arenes To Be Nonplanar" Damian Moran, Andrew C. Simmonett, Franklin E. Leach III, Wesley D. Allen, = Paul v. R. Schleyer, and Henry F. Schaefer III J. AM. CHEM. SOC. 2006, 128, 9342-9343 Dr. Russell D. Johnson III Research Chemist National Institute of Standards and Technology Computational Chemistry Group 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 Sent to CCL by: "Minho Kim" [astro33-#-ajou.ac.kr] Hello! I calculated ground state of phenol using HF & MP2 method. HF method calculated well, but MP2 has a big problem. Freq. Calc. result has an imagenary number, so vibration frequency has minu= s value. I calculated several geometry of phenol, but they converged same result. why did't MP2 method calculate well? How can I do? From owner-chemistry@ccl.net Thu Jun 4 14:13:00 2009 From: "Ol Ga eurisco1-#-pochta.ru" To: CCL Subject: CCL: please help me. Message-Id: <-39436-090604133312-10232-9sqZuwD+KbU4VjNwIPVWSA++server.ccl.net> X-Original-From: "Ol Ga" Date: Thu, 4 Jun 2009 13:33:08 -0400 Sent to CCL by: "Ol Ga" [eurisco1!=!pochta.ru] Dear Minho Kim, You got well known artificial result (non-planar benzene ring) by using correlated method (MP2) with un-correlated basis set (6-31++G*). Please, have a look at the article Popular Theoretical Methods Predict Benzene and Arenes To Be Nonplanar Damian Moran,* Andrew C. Simmonett, Franklin E. Leach III, Wesley D. Allen,* Paul v. R. Schleyer,* and Henry F. Schaefer III; ; Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, and School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia J. Am. Chem. Soc., 2006, 128 (29), pp 93429343 DOI: 10.1021/ja0630285 It is necessary to use Correlation consistent basis sets. Sincerely, Ol Ga > Sent to CCL by: "Minho Kim" [astro33-#-ajou.ac.kr] > Hello! > I calculated ground state of phenol using HF & MP2 method. > HF method calculated well, but MP2 has a big problem. > Freq. Calc. result has an imaginary number, so vibration frequency has minus value. > I calculated several geometry of phenol, but they converged same result. > why did't MP2 method calculate well? How can I do? > Sorry, my English is very poor. Thank you for read. > ----------------------------------------------- > You can get LOG file. > http://astrostars.v3webhard.com/chemical/phenol_opt7.log From owner-chemistry@ccl.net Thu Jun 4 18:31:00 2009 From: "Iain Wallace iain.m.wallace::gmail.com" To: CCL Subject: CCL: Database of Natural substrates Message-Id: <-39437-090604175729-5651-vOKITbvbVlvDirihK9C+4w*|*server.ccl.net> X-Original-From: Iain Wallace Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 04 Jun 2009 16:57:48 -0400 MIME-Version: 1.0 Sent to CCL by: Iain Wallace [iain.m.wallace-,-gmail.com] Hi All, I was wondering if anybody knows of a database where I could get a list/structures of natural substrates (not products), like ATP or ethanol. I am trying to separate a list of compounds into natural substrates or not from the STITCH database. The closest I could find is the BRENDA database, but that is proving to be quite hard to parse, and the ZINC database doesn't have anything like this. Thanks for any pointers, Iain From owner-chemistry@ccl.net Thu Jun 4 23:32:00 2009 From: "Yutao Yue Yutao.Yue*_*gmail.com" To: CCL Subject: CCL: PH-dependent ab-initio calculations Message-Id: <-39438-090604232325-24556-esAULNRVyQdt+/YZBEzV1Q]|[server.ccl.net> X-Original-From: "Yutao Yue" Date: Thu, 4 Jun 2009 23:23:20 -0400 Sent to CCL by: "Yutao Yue" [Yutao.Yue^_^gmail.com] Hello dear friends, does anybody know how to do an ab-initio calculation of a molecular system under a certain PH value? Has there been much development on PH-dependent ab-initio methods? Maybe some PH-dependent empirical methods? Thanks for any information. Regards, Yutao Yue