From owner-chemistry@ccl.net Fri Apr 4 07:53:00 2014 From: "Barry Hardy barry.hardy(0)vtxmail.ch" To: CCL Subject: CCL: eCheminfo drug discovery workshop, Oxford, 21 - 25 July Message-Id: <-49892-140404074908-1565-pSW5TVuO/oW7WPUf2+M8+Q~!~server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 04 Apr 2014 13:49:00 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy|vtxmail.ch] We are holding the next eCheminfo community of practice hands-on drug discovery workshop in Oxford, 21 - 25 July. http://www.douglasconnect.com/events/echeminfo-2014 As in previous workshops the emphasis is on problem solving, practical hands-on use of methods and software applied to drug discovery problems, and working together throughout the week. The workshop will also offer a neglected disease case study focus. We are open for Bursary applications through 18 April: http://echeminfo.com/bursaryDD14 best regards Barry Hardy eCheminfo Community of Practice Douglas Connect GmbH Baermeggenweg 14 4314 Zeiningen Switzerland From owner-chemistry@ccl.net Fri Apr 4 08:27:00 2014 From: "Alan Shusterman alan|a|reed.edu" To: CCL Subject: CCL: Electrostatic potential vs Electrostatic potential mapping Message-Id: <-49893-140404013859-9208-idjr5HF6EhHiYKDiQm8/BQ{=}server.ccl.net> X-Original-From: Alan Shusterman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 03 Apr 2014 22:38:50 -0700 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan[*]reed.edu] Dear Dr. Ajayakumar, The short answer is comparisons of potentials produced by ions and neutrals can be useful, but it can also be confusing because the potentials are dominated by the excess charge. Even a neutral molecule and a neutral salt can look quite different. Some of this becomes obvious if you consider the entire molecule as a point in space. An uncharged molecule will produce potentials of zero everywhere. A charged molecule, however, will produce large non-zero potentials so the excess charge has a large effect. Here is a comparison of three potential maps for you: https://www.dropbox.com/s/ayh4vvr4wsplfh8/2014-04-03_1024_Ajayakumar.png (I hope this URL will go through CCL. If not, I will send the image to you directly. Please download the image within the next 48 hours because I will delete it after that.) The image shows B3LYP/6-31G* electrostatic potential maps of C6H5ONa (left, red arrow points to Na), C6H5O anion (center) and C6H5OH neutral (right, yellow arrow points to H of OH). All three maps are colored on the same scale (see legend at left). Notice that the colors on the anion map are much more negative than those on the ion pair and neutral molecule maps. The excess charge dominates the anion's potential so a CH looks very negative in the anion and much closer to neutral in the other models. Best wishes, Alan On Wed Apr 2 23:29:24 2014, ajay mr mr.ajay.mr/./gmail.com wrote: > Dear Prof. Alan Shusterman, > > I highly appreciate your time and support. your reply very much helped > me to understand some of the critical aspects of ESP. Thank you for > the help. Please let me ask one more doubt. Is there any issues > related to the ESP plots of aromatic molecules (say, Benzene) having > an anionic or cationic substituent? As an example, Phosphonium-Benzene > is a cationic system. Can we plot the ESPs of this system without > considering the counter ion (say, bromide)? > > Thanking you > > Dr. M. R. Ajayakumar > School of Physical Sciences > Jawaharlal Nehru University > New Delhi - 110 067 > https://sites.google.com/site/mrajayakumarjnu/home > http://www.jnu.ac.in/Faculty/pritam/home.html > > > On Sun, Mar 30, 2014 at 2:11 AM, Alan Shusterman alan%x%reed.edu > > wrote: > > > Sent to CCL by: Alan Shusterman [alan],[reed.edu ] > Dear Dr. Ajayakumar, > > I believe your question 1) is asking about the difference between > an electrostatic potential *isosurface* and an electrostatic > potential *map*. > > Because the electrostatic potential varies from one point in space > to the next, there are many ways to present information about > potentials. An isosurface shows points at which the potential is > the same. A map shows how the potential varies across some > arbitrarily chosen surface. > > If this is confusing, consider this analogy. Temperature, like > potential, varies with position. If we measure the temperatures > around a pot of boiling water, we could show our results by > choosing one temperature value (say 30C) and showing all of the > points in space where our thermometer reads this temperature > (probably these would be points far away from the pot). This would > be a temperature isosurface. Or, we could define an arbitrary > surface (say the surface of the pot or the pot's lid), and ask how > the temperature varies on this surface. There would be a range of > temperatures on this surface and we would use a colored map to > show the variation in temperature. > > Turning to question 2), there are several numbers that are used to > describe these two types of images. > For an isosurface, you need to say what value of the potential was > chosen. Returning to my analogy, a 60C isosurface would be much > more compact and located closer to the boiling water than a 30C > isosurface, so the temperature would need to be provided. > For a map, you need to say how the surface was chosen (a common > choice is to use a surface where the electron density = 0.002 au) > and then provide a legend for translating potentials into map > colors. Many potentials provide only the extreme values of the > legend and not the intermediate values. So when you see a range > like -1.24 to +1.24, this is saying that potentials that are <= > -1.24 are assigned a color at one extreme (often red) and > potentials >= +1.24 are assigned a color at the other extreme > (often dark blue). The extreme values, though, don't tell you how > to interpret other colors. > > As for 3) it is usually a good idea to use the same > potential-to-color mapping for all of your maps. There is no > standard way to do this, but here are two choices to consider for > comparing two D-A systems. > Choice #1 - adjust the colors so that the full range of potentials > in the *more polar* DA system can be observed (that is, no > potentials fall outside the color range). Applying this same > mapping for the *less polar* DA system will create a map with > fewer colors and the colors will be dominated by the middle of the > potential-to-color legend (often green). > Choice #2 - adjust the colors so that the full range of potentials > in the *less polar* DA system can be observed. Now the colors on > both maps will span the full color spectrum, but the *more polar* > DA system can still be identified because it will have larger > regions colored with the extreme colors (large red and/or dark blue?). > > 4) I use Spartan (www.wavefun.com ). It's > very easy to learn and use. It is not free, but there are a > variety of packages with different prices > > Best wishes, > Alan > > On 3/28/14 11:57 PM, ajay mr mr.ajay.mr- -gmail.com > wrote: > > Dear CCL subscribers, > > I was confused for a long time about the > representation/visualization of electrostatic potential (ESP) > surface (or mapping). In many litterateurs I saw the authors > are describing the electron density differences of various > motifs in an aromatic molecule, say, donor- acceptor (D-A) > kind of molecule. Using this surface plots they could easily > establish the electronic nature similar kind of systems (a > class of D-A molecules). > > My doubts are, > 1) Difference between Electrostatic potential and > electrostatic potential mapping?? > 2) What is the significance of the scale of the surface plots > (e.g. -1.24 to +1.24 eV)?? > 3) If I want to compare a set of similar D-A systems, whether > I plot all the ESP mapped figures in a same scale? > 4) Which are the best softwares (apart from GaussView) for ESP > surface plots (preferably freewares)? > > Looking for your kind support. > > Thanking you, > > Dr. M. R. Ajayakumar > School of Physical Sciences > Jawaharlal Nehru University > New Delhi - 110 067 > https://sites.google.com/site/__mrajayakumarjnu/home > > http://www.jnu.ac.in/Faculty/__pritam/home.htmlDear > subscribers, > > > -- > Alan Shusterman > Chemistry Department > Reed College > 3203 SE Woodstock Blvd. > Portland, OR 97202-8199 > 503-517-7699 > http://blogs.reed.edu/alan/ > "Nature doesn't make long speeches." Lao Tzu 23 > > > > -= This is automatically added to each message by the mailing > script =- > E-mail to subscribers: CHEMISTRY[#]ccl.net > or use: > http://www.ccl.net/cgi-bin/__ccl/send_ccl_message > > > E-mail to administrators: CHEMISTRY-REQUEST[#]ccl.net > or use > http://www.ccl.net/cgi-bin/__ccl/send_ccl_message > > http://www.ccl.net/chemistry/__sub_unsub.shtmlConferences: > http://server.ccl.net/__chemistry/announcements/__conferences/ > > > Search Messages: > http://www.ccl.net/chemistry/__searchccl/index.shtml > > http://www.ccl.net/spammers.__txt > > RTFI: http://www.ccl.net/chemistry/__aboutccl/instructions/ > > > > -- Alan Shusterman Chemistry Department Reed College 3203 SE Woodstock Blvd Portland, OR 97202-8199 503-517-7699 http://blogs.reed.edu/alan/ "Nature doesn't make long speeches." Lao Tzu 23 From owner-chemistry@ccl.net Fri Apr 4 09:54:00 2014 From: "James Prudhomme jprudhomme _ healthtech.com" To: CCL Subject: CCL: Structure- and Dynamics-Based Design Strategies Message-Id: <-49894-140404080947-7974-tObad7x9ufgPNy3mD5hV4w|*|server.ccl.net> X-Original-From: "James Prudhomme" Date: Fri, 4 Apr 2014 08:09:45 -0400 Sent to CCL by: "James Prudhomme" [jprudhomme(0)healthtech.com] Dinner Short Course, Organized by Cambridge Healthtech Institute (CHI): Structure- and Dynamics-Based Design Strategies Tuesday, May 20 | 6:00-9:00 pm Westin Boston Waterfront, Boston, MA This course will reveal design strategies that led to drugs currently in the clinic and on the market. An emphasis will be made on the exploitation of the bioactive ligand conformations using combinations of NMR, X-ray, calculations and SAR. Rational design and the implications of other properties will be addressed which include atropisomer chirality, drug self-aggregation and ADMET. This course will be held prior to the start of the 14th annual Structure-Based Drug Design (SBDD) conference being held on May 21-22. Instructors: Steven LaPlante, Ph.D., Founder & CEO, NMX Research & Solutions; Adjunct Professor, Institut National de la Recherche Scientifique (INRS) Chris Williams, Ph.D., Principal Scientist, Chemical Computing Group Detailed Agenda: 6:00 Dinner Served 6:15 Strategies for Drug Design Starting from Peptides, HTS Hits and Small-Molecule Fragments Steven LaPlante, Ph.D., Founder & CEO, NMX Research & Solutions; Adjunct Professor, Institut National de la Recherche Scientifique (INRS) 7:15 Coffee Break 7:45 Designing Inhibitors with MOE Structure-Based Drug Design Tools Chris Williams, Ph.D., Principal Scientist, Chemical Computing Group 8:45 Q&A with Speakers 9:00 Close of Course. How to Register: Web: https://chidb.com/register/2014/sbd/reg.asp Call: 781-972-5400 Email: reg^healthtech.com For details and to register for the SBDD conference, visit www.healthtech.com/structure-based-drug-design. For questions, contact: James Prudhomme Senior Marketing Manager Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 Direct: 781-972-5486 jprudhomme^healthtech.com