From owner-chemistry@ccl.net Tue Oct 10 09:07:00 2006 From: "Barry Hardy barry.hardy^^tiscalinet.ch" To: CCL Subject: CCL: Could we take a Community Approach to Comparing Virtual Screening Methods? Message-Id: <-32746-061010084425-32616-0RV0CDvne+240WkrS5kLog%x%server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="=====================_11772999==_.ALT" Date: Tue, 10 Oct 2006 13:47:14 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy]~[tiscalinet.ch] --=====================_11772999==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed John Irwin at UCSF, I and others working in the area of drug discovery have had several recent discussions and email exchanges on the topic of the performance and comparison of different virtual screening and docking methods on different targets and problems. We thought it would be useful to summarise some ideas on supporting greater collaboration on such work and to invite comments and discussion. Please visit our blog post to access our summary and references and to provide feedback at: Could we take a Community Approach to Comparing Virtual Screening Methods? http://barryhardy.blogs.com/cheminfostream/2006/10/could_we_take_a.html In the upcoming eCheminfo Community of Practice meeting at Bryn Mawr (16-19 October) we have scheduled related workshop activities on virtual screening and docking and a forum to discuss whether a collaborative project to benchmark docking programs is of interest, and if so, how to best move forward. More Information at: http://www.innovationwell.net/COMTY_screening/ As certainly not everyone interested in this topic can be present at the meeting at Bryn Mawr, and time there is limited, we welcome feedback on the blog post or by email before the meeting. best regards Barry Hardy eCheminfo Community of Practice Manager http://echeminfo.colayer.net/ +41 61 851 0170 --=====================_11772999==_.ALT Content-Type: text/html; charset="us-ascii" John Irwin at UCSF, I and others working in the area of drug discovery have had several recent discussions and email exchanges on the topic of the performance and comparison of different virtual screening and docking methods on different targets and problems.  We thought it would be useful to summarise some ideas on supporting greater collaboration on such work and to invite comments and discussion.  Please visit our blog post to access our summary and references and to provide feedback at:

Could we take a Community Approach to Comparing Virtual Screening Methods?
http://barryhardy.blogs.com/cheminfostream/2006/10/could_we_take_a.html

In the upcoming eCheminfo Community of Practice meeting at Bryn Mawr (16-19 October) we have scheduled related workshop activities on virtual screening and docking and a forum to discuss whether a collaborative project to benchmark docking programs is of interest, and if so, how to best move forward. More Information at:
http://www.innovationwell.net/COMTY_screening/

As certainly not everyone interested in this topic can be present at the meeting at Bryn Mawr, and time there is limited, we welcome feedback on the blog post or by email before the meeting.

best regards
Barry Hardy
eCheminfo Community of Practice Manager
http://echeminfo.colayer.net/
+41 61 851 0170
--=====================_11772999==_.ALT-- From owner-chemistry@ccl.net Tue Oct 10 10:26:01 2006 From: "sari souad sari_souad _ yahoo.fr" To: CCL Subject: CCL: dielectric constant Message-Id: <-32747-061009051128-1236-9Ku9DrtZGa/wq7zha+Pfhw::server.ccl.net> X-Original-From: "sari souad" Date: Mon, 9 Oct 2006 05:11:27 -0400 Sent to CCL by: "sari souad" [sari_souad#,#yahoo.fr] I want to know the electric constant of 1M HCl.thanks From owner-chemistry@ccl.net Tue Oct 10 14:19:00 2006 From: "Hemant Kr Srivastava hemantkrsri() gmail.com" To: CCL Subject: CCL: PCM vs. explicit water with PCM - effect on reaction profile Message-Id: <-32748-061010104258-700-rNabDCjNpjqL7SYZZ8JKWQ###server.ccl.net> X-Original-From: "Hemant Kr Srivastava" Date: Tue, 10 Oct 2006 10:42:57 -0400 Sent to CCL by: "Hemant Kr Srivastava" [hemantkrsri+*+gmail.com] Dear CCL Users, I am calculating the barrier for a reaction in solution using two different mechanisms. Both mechanisms share the same first step. Since one of the mechanisms (mechanism-2) involves an explicit water molecule, I have optimized all the structures for the first mechanism (mechanism-1) in following two ways. 1- Optimization in PCM by using scrf=(solvent=water,pcm) 2- Optimization by adding one explicit water molecule using same keyword. But I am getting very different profiles for mechanism-1 in those two cases (see below), I understand that PCM does not account for all the effect of the solvent, however, the differences seem too large. I will be grateful to you if you will help me to understand the problem. following are the results for mechanism-1 level of calculation: B3LYP/6-31g* with PCM TS1 Inter1 TS2 Inter2 with explicit water 12.7 11.0 15.9 -41.2 without explicit water 9.2 4.6 16.6 -43.6 results are given in kcal/mol relative to the energy of the reactant's complex. (I did also calculations of free energy thinking that the entropy is important here but it did not change the results much) Thanking you, Best regards, Hemant ============================================ Dr. Hemant Kumar Srivastava, Postdoctoral Fellow, Department of Medicinal Chemistry and Natural Products, School of Pharmacy, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, Jerusalem - 91120, ISRAEL, Phone- +972-2-6757495, Fax- 972-2-6757076, Cell- +972-546582016, Email- hemantkrsri]-[gmail.com ================================================================== From owner-chemistry@ccl.net Tue Oct 10 14:58:01 2006 From: "Gonzalo Jimenez Oses gonzalo.jimenez*_*dq.unirioja.es" To: CCL Subject: CCL: PCM vs. explicit water with PCM - effect on reaction profile Message-Id: <-32749-061010145707-28556-Hgy/nodtYijSnfRONwBHdA^server.ccl.net> X-Original-From: "Gonzalo Jimenez Oses" Date: Tue, 10 Oct 2006 14:57:07 -0400 Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez+*+dq.unirioja.es] Dear CCL'ers I am also very interesting in the differences emerging from introducing one or more explicit solvent molecules in PCM calculations (or any other continuum models). I also asked something related to this question, and probably the most valuable answer I obtained was offered by Dr. Frank Jensen (thank you!): "One thing to consider is that PCM type models are parameterized models, and the values of the parameters have been derived to fit experiments, _without_ an explicit first solvation shell. A large fraction of solvation is the first shell, and that has been absorbed by the parameters. Introducing an explicit solvation shell and then put a PCM on top of that may therefore give you a kind of double counting. Of course the cavity changes, and there are the usual problems of electron density outside the cavity, etc.... In short, there is a risk that the results will _deteriorate_ when putting in an explicit first solvation shell. I am not aware of any study where the performance of PCM type models where the first solvation shell is considered explicitly, but if you find any, I would appreciate the reference(s). In principle such an approach should be able to provide more accurate results than a pure continuum model, but the PCM parameters may have to be returned. This, of course, is not trivial, and the optimal set of parameters may depend on which method you use for the solvent molecules (HF, DFT, MP2, etc). Sorting this out should keep you busy for a while ;-)" I hope this could help a little. In my experience, this kind of discrepancies are much more accusated in the case of charged molecules, in which the inclusion of solvent effects are usually needed. When possible, a good alternative should include one or more counterions to neutralize the charges. In any case, I recommend you to read the interesting posts coming from Prof. Andreas Klamt (COSMO model), which is an expert on this field. Best regards, Gonzalo > Sent to CCL by: "Hemant Kr Srivastava" [hemantkrsri+*+gmail.com] > Dear CCL Users, > > I am calculating the barrier for a reaction in solution using two different mechanisms. Both mechanisms share the same first step. Since one of the mechanisms (mechanism-2) involves an explicit water molecule, I have optimized all the structures for the first mechanism (mechanism-1) in following two ways. > 1- Optimization in PCM by using scrf=(solvent=water,pcm) > 2- Optimization by adding one explicit water molecule using same keyword. > > But I am getting very different profiles for mechanism-1 in those two cases (see below), I understand that PCM does not account for all the effect of the solvent, however, the differences seem too large. I will be grateful to you if you will help me to understand the problem. > > following are the results for mechanism-1 > level of calculation: B3LYP/6-31g* with PCM > > TS1 Inter1 TS2 Inter2 > with explicit water 12.7 11.0 15.9 -41.2 > without explicit water 9.2 4.6 16.6 -43.6 > > results are given in kcal/mol relative to the energy of the reactant's complex. > > (I did also calculations of free energy thinking that the entropy is important here but it did not change the results much) > > Thanking you, > > Best regards, > Hemant > ============================================ > Dr. Hemant Kumar Srivastava, Postdoctoral Fellow, > Department of Medicinal Chemistry and Natural Products, > School of Pharmacy, Faculty of Medicine, Ein Kerem Campus, > The Hebrew University of Jerusalem, Jerusalem - 91120, ISRAEL, > Phone- +972-2-6757495, Fax- 972-2-6757076, Cell- +972-546582016, > Email- hemantkrsri^gmail.com > ================================================================== > > From owner-chemistry@ccl.net Tue Oct 10 15:32:00 2006 From: "Shobe, David David.Shobe * sud-chemie.com" To: CCL Subject: CCL: PCM vs. explicit water with PCM - effect on reaction profile Message-Id: <-32750-061010151527-12712-zR8JNX55YSzZ/Ct6xuCJMg-x-server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 10 Oct 2006 21:15:07 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe::sud-chemie.com] The question I would ask myself is: What is the water molecule "doing" during this reaction? (Is it forming a hydrogen bond as donor or receiver, or perhaps acting as a nucleophile? Or is it more or less a spectator?) --David Shobe Süd-Chemie, Inc. -----Original Message----- > From: owner-chemistry * ccl.net [mailto:owner-chemistry * ccl.net] Sent: Tuesday, October 10, 2006 2:40 PM To: Shobe, David Subject: CCL: PCM vs. explicit water with PCM - effect on reaction profile Sent to CCL by: "Hemant Kr Srivastava" [hemantkrsri+*+gmail.com] Dear CCL Users, I am calculating the barrier for a reaction in solution using two different mechanisms. Both mechanisms share the same first step. Since one of the mechanisms (mechanism-2) involves an explicit water molecule, I have optimized all the structures for the first mechanism (mechanism-1) in following two ways. 1- Optimization in PCM by using scrf=(solvent=water,pcm) 2- Optimization by adding one explicit water molecule using same keyword. But I am getting very different profiles for mechanism-1 in those two cases (see below), I understand that PCM does not account for all the effect of the solvent, however, the differences seem too large. I will be grateful to you if you will help me to understand the problem. following are the results for mechanism-1 level of calculation: B3LYP/6-31g* with PCM TS1 Inter1 TS2 Inter2 with explicit water 12.7 11.0 15.9 -41.2 without explicit water 9.2 4.6 16.6 -43.6 results are given in kcal/mol relative to the energy of the reactant's complex. (I did also calculations of free energy thinking that the entropy is important here but it did not change the results much) Thanking you, Best regards, Hemant ============================================ Dr. Hemant Kumar Srivastava, Postdoctoral Fellow, Department of Medicinal Chemistry and Natural Products, School of Pharmacy, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, Jerusalem - 91120, ISRAEL, Phone- +972-2-6757495, Fax- 972-2-6757076, Cell- +972-546582016, Email- hemantkrsri^gmail.com ==================================================================http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Tue Oct 10 19:10:00 2006 From: "T-Tsuru coral t-tsuru]-[coral.dti.ne.jp" To: CCL Subject: CCL:G: PM3 parameters Message-Id: <-32751-061010184121-31796-h/cEFrxCEm9B7ekYPGNW5A.@.server.ccl.net> X-Original-From: "T-Tsuru coral" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-2022-jp" Date: Wed, 11 Oct 2006 06:54:20 +0900 MIME-Version: 1.0 Sent to CCL by: "T-Tsuru coral" [t-tsuru . coral.dti.ne.jp] Hello, CCLers. I like to know the parameters which play important roll of electron correlation in PM3 method. I've read Stewart's PM3 paper (J.Comp.Chem. 10, p209, 1989) and know there are 18 parameters each atom (Hydrogen is 11.) But I can't find suitable parameters from them. The description of the parameters for electron correlation of this paper is: In other words, the correlation effects, which in ab initio methods require extensive calculations of the Meiller-Plesset type, can, at the MNDO level of approximation, be represented by simple gaussian functions. I can't imagine the relationship between the parameters and gaussian functions. PM3 is derived from MNDO method. In the point of view of the parameter's meaning, there are common parameters between PM3 and MNDO. So I've read several articles of MNDO, but I can't find the suitable description too. If you know such PM3 parameters or article description, please teach me. When I receive the replies, I will summarize them and send to CCL. Thanks. Sincerely yours, ---------------------------------------------------- Telkuni Tsuru t-tsuru * coral.dti.ne.jp Bunshi Gijyutu From owner-chemistry@ccl.net Tue Oct 10 19:45:00 2006 From: "Agalya G agalya81-,-gmail.com" To: CCL Subject: CCL: Ionization potential and Electron affinity of Donor-Acceptor system Message-Id: <-32752-061010192633-16702-2Z2evf40bvRHciCvbCNepA|*|server.ccl.net> X-Original-From: "Agalya G" Date: Tue, 10 Oct 2006 19:26:33 -0400 Sent to CCL by: "Agalya G" [agalya81{:}gmail.com] Dear CCL users, Can anyone tell me how to calculate ionization potential of donor and electron affinity of acceptor in donor-acceptor system? In one journal in have seen, that they mentioned HOMO energy as the ionization potential of donor and LUMO energy as the electron affinity of acceptor. Is that the correct way of calculating ionization potential of donor and electron affinity of acceptor in donor-acceptor system? Kinldy give me your suggestions. With Regards, Agalya From owner-chemistry@ccl.net Tue Oct 10 23:10:00 2006 From: "zainurul izwan ismail zainurulizwan80::yahoo.com" To: CCL Subject: CCL: x-ray crystal structure Message-Id: <-32753-061010230513-9505-CppTkjxVkPjXbJ0+0eMTIg++server.ccl.net> X-Original-From: "zainurul izwan ismail" Date: Tue, 10 Oct 2006 23:05:12 -0400 Sent to CCL by: "zainurul izwan ismail" [zainurulizwan80++yahoo.com] Dear all, I'm having problem to get x-ray crytal structure for this compound a. asiatic acid b. madecassic acid c. madecassoside. Can someone sent to me any journal(name) that provide x-ray crystal structure for these compound. Thanks in advance. Regards, -Izwan.