From owner-chemistry@ccl.net Thu Nov 3 03:08:00 2005 From: "Perumal Gurusamy gurusamy2k5|,|yahoo.com" To: CCL Subject: CCL: Calculation of PES Message-Id: <-29867-051103030437-1126-v6lGafrV6RatJ+nivftnTA(!)server.ccl.net> X-Original-From: "Perumal Gurusamy" Sent to CCL by: "Perumal Gurusamy" [gurusamy2k5-#-yahoo.com] Dear CCLers, Greetings! I'm very new to this area. I'm Interested in studying the conformational aspects of various amino acids and need to plot PES. I'm facing problem in constructing a PES. Could anyone explain me the procedures of getting a PES on G-98/G-View or other free softwares. Any Tutorials/PPTs/PDFs will be of much useful. Thanking you for your help and i promise that i will summarise at the end. Regards, P.Gurusamy, gurusamy2k5*_*yahoo.com From owner-chemistry@ccl.net Thu Nov 3 04:27:01 2005 From: "Noel O Boyle no228;;cam.ac.uk" To: CCL Subject: CCL: XYZ grad to internal gradients Message-Id: <-29868-051103042440-10627-steYR7b9dvBMAW9QR5Mn3g-*-server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 03 Nov 2005 09:24:21 +0000 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228{=}cam.ac.uk] This is the sort of thing that you may find in an open-source computational chemistry package (if you are not worried about the quality control :-). At the moment, I am aware of three open-source packages: PyQuante, GAMESS and MPQC (use Google). Regards, Noel. On Wed, 2005-11-02 at 15:46 +0000, jmmckel~~attglobal.net wrote: > Sent to CCL by: jmmckel-$-attglobal.net > Hello.. > > I have a set of cartesian coordinates and the corresponding cartesian > gradients, and the connectivities for each atom in a Z-matrix form. Can > someone point me to a routine or two that can be adapted to convert the > cartesian gradients into internal gradients? > > Many thanks, > > John McKelvey> > > From owner-chemistry@ccl.net Thu Nov 3 05:40:01 2005 From: "Barry Hardy barry.hardy##tiscalinet.ch" To: CCL Subject: CCL: Program/Schedule for European eCheminfo InterAction meeting (November 9,10) Message-Id: <-29869-051103053755-15519-UGblJhHCRhLlm/aY0tUb9g.@.server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="=====================_8654308==_.ALT" Date: Thu, 03 Nov 2005 10:42:33 +0100 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy _ tiscalinet.ch] --=====================_8654308==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed The European eCheminfo InterAction meeting "Applications of Cheminformatics and Chemical Modelling to Drug Discovery" takes place in Basel, Switzerland next week (November 9-10). The schedule with list of presentations and discussion sessions is available at: http://echeminfo.colayer.net/files/SpeakerTopcSchedule-IA05-Basel-v5.pdf The eCheminfo meeting runs concurrently with our InnovationWell Community meeting; registrants are welcome to attend sessions from either program. Further details, such as abstracts and speaker bios, can be viewed in the Program areas of either the http://innovationwell.net/ or the echeminfo.com websites. We will be closing registrations shortly, so please let us know quickly if you'd like to come. Register through the websites or contact Nicki Douglas (nicki.douglas at douglasconnect.com, +41 61 851 04 61) And if you can't make the meeting, you can access the recordings and presentation materials if you become a member of one of these communities. You will also have access to all previous sessions (including those from last month's US InterAction meetings in Philadelphia being released this month). Best regards, Barry Hardy Community of Practice Manager Douglas Connect, Switzerland tel: +41 61 851 0170 --=====================_8654308==_.ALT Content-Type: text/html; charset="us-ascii" The European eCheminfo InterAction meeting "Applications of Cheminformatics and Chemical Modelling to Drug Discovery" takes place in Basel, Switzerland next week (November 9-10).  The schedule with list of presentations and discussion sessions is available at:
http://echeminfo.colayer.net/files/SpeakerTopcSchedule-IA05-Basel-v5.pdf

The eCheminfo meeting runs concurrently with our InnovationWell Community meeting; registrants are welcome to attend sessions from either program.  Further details, such as abstracts and speaker bios, can be viewed in the Program areas of either the http://innovationwell.net/ or the echeminfo.com websites.

We will be closing registrations shortly, so please let us know quickly if you'd like to come.  Register through the websites or contact Nicki Douglas (nicki.douglas at douglasconnect.com, +41 61 851 04 61)

And if you can't make the meeting, you can access the recordings and presentation materials if you become a member of one of these communities. You will also have access to all previous sessions (including those from last month's US InterAction meetings in Philadelphia being released this month).

Best regards,
Barry Hardy
Community of Practice Manager
Douglas Connect, Switzerland
tel: +41 61 851 0170 --=====================_8654308==_.ALT-- From owner-chemistry@ccl.net Thu Nov 3 07:39:01 2005 From: "Telkuni Tsuru telkuni[]venus.dti.ne.jp" To: CCL Subject: CCL: Summary-- Circular Dichroism (CD) Message-Id: <-29870-051103073440-3596-i3t/Y4uE2wpkL3sFcf5f+g_+_server.ccl.net> X-Original-From: "Telkuni Tsuru" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-2022-jp" Date: Thu, 3 Nov 2005 21:34:52 +0900 MIME-Version: 1.0 Sent to CCL by: "Telkuni Tsuru" [telkuni]_[venus.dti.ne.jp] Hello, CCLers. I've sent following question which relate to circular dichroism(CD). ----- Original Question ----- > I like to know the relationship between the circular dichroism(CD) > and quantum chemistry. > > I've tried to retrieve the books and web-sites which describe the > mechanism of the CD with the view point of quantum chemistry(or > with quantum chemical words), but I can't find suitable document. > > Could you recommend me some good papers or web-sites which > describe the CD with quantum chemical words ? > > When I get replies, I will summarize them and upload to this ML. I've received good replies. Thank you so much to whom send the reply. Now I'm reading the recommended articles. Here is the summary. 1) from Mariusz Sterzel -------------- Hello, I would also suggest: E. U. Condon Rev. Mod. Phys. 9, 432-457 (1937). Henry Eyring, Han-Chung Liu, Dennis Caldwell; Chem. Rev.; 1968; 68(5); 525-540. Walter J. Kauznman, John E. Walter, Henry Eyring; Chem. Rev.; 1940; 26(3); 339-407. Mariusz 2) from Daniel Crawford -------------- [Sorry. His pdf is omitted.] Telkuni, I have just written a review article summarizing quantum chemical evaluation of various chiro-optical properties, including CD. I've attached a preprint of the paper, which is in press in Theoretical Chemistry Accounts. -Daniel Crawford 3) from Marcel Swart -------------- See the website of Jochen Autschbach where many papers deal with CD spectra: http://www.nsm.buffalo.edu/~jochena/publications/publications.html ---- dr. Marcel Swart Theoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart-#-few.vu.nl Web http://www.few.vu.nl/~swart 4) from Rajan Vatassery -------------- Dear Dr Tsuru, I found "circular dichroic spectroscopy, exciton coupling in organic stereochemistry" by Harada/Nakanishi extraordinarily helpful. it is however, a bit too basic for many concepts but the references within (especially Condon's) are quite insightful. unfortunately the most useful reference in there is Rosenfeld's 1928 article in Z Phys, which is in german. it is also not available (to my knowledge) online as apparently nobody has scanned it in. in the above harada/nakanishi book, chapters 1 and 10 are the only ones germane to your interest. good luck and let me know (on the ML) if you find a particularly good reference. raj 5) from Olli Lehtonen -------------- Hi, I was also recently looking for a similar thing. Here are a couple references I found useful. Both basic theoretical aspects and applications of CD are covered in a book Circular Dichroism: Principles and Applications, 2nd Edition Nina Berova, Koji Nakanishi, Robert W. Woody Wiley-VCH (2000) Technical things how to calculate CD spectra using time-dependent DFT can be found in article An improved method for density functional calculations of the frequency-dependent optical rotation Grimme S, Furche F, Ahlrichs R CHEMICAL PHYSICS LETTERS 361 (3-4): 321-328 JUL 30 2002 I'm looking forward to your summary. regards, Olli Lehtonen ---------------------------------------------------- Telkuni Tsuru telkuni%x%venus.dti.ne.jp Bunshi Gijyutu From owner-chemistry@ccl.net Thu Nov 3 09:12:00 2005 From: "yang zhen na yangzn553::nenu.edu.cn" To: CCL Subject: CCL: intramolecular proton transfer Message-Id: <-29871-051103090948-15742-1b0gFmq+9LKAduNV6os+8g*|*server.ccl.net> X-Original-From: "yang zhen na" Sent to CCL by: "yang zhen na" [yangzn553[]nenu.edu.cn] I calculate the proton transfer reaction of a molecule, the experiment revealed that in the ground state the enol form is more stable than the keto form, but in the excited state keto form is more stable than the enol form. First, the energy of the excited state was obtained by summing the energy of the ground state and the corresponding excitation energy. And get the conclusion that keto form is more stable the enol form in the first excited state. Sencod, I optimize the geometries of two forms in the excited state using cis method and find the energy by keywords scf done. But the conclusion is that enol form is more stable than the keto form. I dont know why different methods get different conclusion and which one is right. The first method is agreement with the experiment value. So I think whether there is two mechanisms for proton transfer in the excited state. First, the proton transfers as the molecule get the excited state and the geometry have not been changed. Second, the molecule relaxes first and then the proton transfers, the molecule I studied is obey the first mechanism. I dont know whether I am right, please help me and give me an answer. I am anxious of getting your help. Think you with the great wishes! From owner-chemistry@ccl.net Thu Nov 3 09:51:00 2005 From: "Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt" To: CCL Subject: CCL: XYZ grad to internal gradients Message-Id: <-29872-051103094748-10082-q409iNbaGSbHsXufAwkKwA:server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 03 Nov 2005 14:47:38 +0000 Mime-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira*o*ist.utl.pt] > On Wed, 2005-11-02 at 15:46 +0000, jmmckel~~attglobal.net wrote: > >>Sent to CCL by: jmmckel-$-attglobal.net >>Hello.. >> >>I have a set of cartesian coordinates and the corresponding cartesian >>gradients, and the connectivities for each atom in a Z-matrix form. Can >>someone point me to a routine or two that can be adapted to convert the >>cartesian gradients into internal gradients? Have you tried openbabel ? cheers, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student {=} IST,Lisbon -- -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.362 / Virus Database: 267.12.7/159 - Release Date: 02-11-2005 From owner-chemistry@ccl.net Thu Nov 3 12:24:00 2005 From: "Dr. N. SUKUMAR nagams^^^rpi.edu" To: CCL Subject: CCL: Summary-- Circular Dichroism (CD) Message-Id: <-29873-051103120118-8605-nUxkbFmo0qo53BW4pJ/AZw{}server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Thu, 03 Nov 2005 12:01:12 -0500 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams * rpi.edu] The book by D.P. Craig and T. Thirunamachandran, "Molecular Quantum Electrodynamics: An Introduction to Radiation-Molecule Interactions" (Academic, London, 1984) contains a good pedagogical exposition of the fundamental quantum mechanics of circular dichroism, magnetic CD and induced CD (in the chapter on Optical Activity). Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From owner-chemistry@ccl.net Thu Nov 3 14:24:00 2005 From: "janl{}speakeasy.net" To: CCL Subject: CCL: Correction: CCG Excellence Award DEADLINE already passed Message-Id: <-29874-051103142212-22508-YrkNgAnrGlSa/OvR9Mp4KA()server.ccl.net> X-Original-From: janl.:.speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 03 Nov 2005 19:22:07 +0000 MIME-Version: 1.0 Sent to CCL by: janl a speakeasy.net Dear CCL, Important correction to the announcement of the Chemical Computing Group and the ACS Division of Computers in Chemistry, 2006 CCG Excellence Award message posted recently on CCL. The DEADLINE for application already passed (Nov. 1, 2005). The message did not give the correct deadline. The winners will be announced on Nov. 15, 2005. Jan Labanowski jkl::ccl.net