From owner-chemistry@ccl.net Wed Dec 15 04:07:01 2010 From: "Chris Swain swain!=!mac.com" To: CCL Subject: CCL: Average Computational Chemistry Contract Research Fees Message-Id: <-43390-101215040605-8306-biu6mXxyruqyiyLnuwqQDw],[server.ccl.net> X-Original-From: Chris Swain Content-transfer-encoding: 7BIT Content-type: text/plain; CHARSET=US-ASCII Date: Wed, 15 Dec 2010 09:05:30 +0000 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain/a\mac.com] Hi, I'm a consultant in medicinal chemistry for the last 5 years and I do some computational chemistry consultancy. You don't say which areas you are looking to undertake consulting in but if it is drug discovery feel free to contact me directly and I'd be happy to share my experiences. Cheers Chris Dr Chris Swain BA MA (Cantab) PhD CChem FRSC Cambridge MedChem Consulting, http://www.cambridgemedchemconsulting.com On 14 Dec 2010, at 16:16, A C Sykes adam.sykes^_^quanano.co.uk wrote: > > Sent to CCL by: "A C Sykes" [adam.sykes(_)quanano.co.uk] > I am looking into branching out into the contract research field. However, I am unsure of the average fees charged for such services, as I am from an academic research background. > > The various companies that offer this service do not publish their fee structures. I am sure quotes are given on a per contract basis, but there has to be a guiding hourly/daily rate which can be used for quoting. > > Thank you for your help.> > From owner-chemistry@ccl.net Wed Dec 15 05:47:00 2010 From: "Eliz Lam elizabeth.shlam:_:gmail.com" To: CCL Subject: CCL: Queries on TDDFT calculations on emission Message-Id: <-43391-101215054529-28500-yjm4+2c6+3xhJ5z1fRW/Hg^server.ccl.net> X-Original-From: "Eliz Lam" Date: Wed, 15 Dec 2010 05:45:21 -0500 Sent to CCL by: "Eliz Lam" [elizabeth.shlam*|*gmail.com] Dear CCLers, Hi, I'm a beginner in learning DFT and TDDFT calculations and have some queries on calculating emission properties of a molecule. I originally thought the emission of a molecule should be the first triplet excited state from TDDFT calculations as stated from Kasha's rule that the emissive state should be of the lowest energy. However, it seems not always the case. I'm wondering why one could not predict emission from the above way and how should one predict the emission of a molecule? And is the emission mechanism originated the same as from first triplet excited state in the TDDFT calculations? Thank you so much! Eliz From owner-chemistry@ccl.net Wed Dec 15 08:49:00 2010 From: "Mohammad Ghattas mah.ghattas,googlemail.com" To: CCL Subject: CCL: H-bonding protein-ligand complexes Message-Id: <-43392-101215042703-20996-r3moOpNO6rHAHcapgBWl0Q..server.ccl.net> X-Original-From: "Mohammad Ghattas" Date: Wed, 15 Dec 2010 04:26:59 -0500 Sent to CCL by: "Mohammad Ghattas" [mah.ghattas=googlemail.com] Dear All, I've got many ligand-protein complexes to analyse but I'm not sure about the H- bond range for a heavy atom to a heavy atom H-bonding as well as hydrogen to a heavy atom H-bonding? and which is always better to consider in publications? Also, is anybody aware of a good paper discusses such topics, including other possible types of interactions in ligand binding (hydrophobic and stacking interactions)? Very best regards, Mohammad From owner-chemistry@ccl.net Wed Dec 15 09:24:00 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis\a/borealisgroup.com" To: CCL Subject: CCL: Average Computational Chemistry Contract Research Fees Message-Id: <-43393-101215024427-13526-QtKyvBRBcANIkg63+rkrjA|,|server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 15 Dec 2010 08:43:59 +0100 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis##borealisgroup.com] Just to add something in the discussion giving some input of someone who has actually crossed to the "dark side" and has a daily experience on how things are working on the "inside". First of all Vincent is absolutely correct on his post and I fully agree with his statements. Furthermore you will need to consider what you are actually offering to your client and how valuable that is to him (this is called value selling in the business lingo - very useful tip for a sales pitch when used properly). What I mean is that most clients although scientifically on a solid basis will have a certain level of difficulty to follow all the details of the theory and the relevant computations. This is not because they're not capable but because they don't usually work with these things on a daily basis. Therefore you need to be in a position to actually gloss over the details and concentrate on the actual outcome and the value it has to the customer. Another thing you need to consider is who are you talking to and adjust your pitch accordingly. Usually the scientific discussion will be conducted with a scientist (junior or senior), but the decision on the actual initiation of the project will be taken by some senior manager with or without any scientific background and appreciation of the level of detail required for the solution you are offering. (the more money you ask the more senior the manager in question) These two discussions will have to approach the problem in a different manner as the decision maker is mostly interested on how much it will cost, why should he pay you (trust me this is the most difficult question to answer) and how he can use what you have to offer. In essence everything boils down to money. If you offer something that your client needs at a reasonable price and you can show that without it he will be losing money he will pay. Another thing to consider is that while working for a customer you will most probably have to sign a non-disclosure agreement which means you cannot publish your findings or use them to impress other clients in the future (there are ways around that but it is not my place to mention them). My advice will be to try to get some information (from conferences or private contacts) on what some of your potential clients are working on (in broad terms) and what are the bottlenecks they are facing. If you do this then you should be able to identify an area where you can actually offer something valuable to them. It is also helpful to speak with scientists working for potential clients as they can be very useful in promoting your cause (but for that you will have to persuade them first - not always that easy) and offer advice on the possible route you can follow. Finally most of the big companies do have close collaborations with Universities around the world, so you can get some information on what they're working on by just checking the literature or even speaking with the academics involved (they will not give you details but you will get a general picture). Finally be prepared to get less money that you were hoping in order to prove to the customer how good and valuable you are. Most customers want to have long-term collaborations and not one-offs, so this can be to your advantage in the long run if you play your cards right. I hope this was helpful, but if you need more information I am more than happy to provide it. Good Luck Thomas Dr Thomas Gkourmpis Researcher - Polyolefin Research Borealis AB | SE-444 86 Stenungsund | Sweden Tel. +46 303 205 576 | Mobile +46 766 378 106 | Fax +46 303 866 49 www.borealisgroup.com | 556078-6633 | Swedish Companies Registration Office ___________________________________ Borealis - Shaping the Future with Plastics -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com*_*ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com*_*ccl.net] On Behalf Of Vincent Leroux vincent.leroux%x%loria.fr Sent: Tuesday, December 14, 2010 10:37 PM To: Gkourmpis, Thomas Subject: CCL: Average Computational Chemistry Contract Research Fees Sent to CCL by: Vincent Leroux [vincent.leroux%x%loria.fr] Tips from an academic who did not yet come to see if the pastures are greener on the other side of the fence (and feeling very uncertain about that, despite currently running out of grass) - for what it is worth You should go to the next big conference and picture yourself as a representative for some company to the stands - not here for signing something big right know, but to check the temperature before reporting to the heads. If you bring some example cases of "things we are considering right now", I guess the Chindian companies will easily give you the median prices as a first proposal. As this is all contract-based, I suppose that in many cases there is no such thing as daily rates - rather more or less stringent deadlines that will influence the price of the whole package. If there are some highly-demanding computations involved, this is another big factor... In any case, the amount of work you will do is nothing - this is all related to the cost of things done internally compared to what you ask for to get the job done... you have to be cheaper, but not too much, or you might not be taken seriously even with some solid references. In addition, you would also have the opportunity to discuss with your possible future clients - feel free to present yourself as an academic then, just curious about things are working on the dark side with all this externalization going on. You might be discouraged by how many possible future clients turn all of a sudden into possible future competitors ;-) In any case, you should have some kind of network in the industry already, or at least know some academics that went there and could provide you with more detailed information. You seem pretty courageous, as to plan turning into a contractor without much experience! Good luck. VL Le 14/12/10 17:16, A C Sykes adam.sykes^_^quanano.co.uk a écrit : > Sent to CCL by: "A C Sykes" [adam.sykes(_)quanano.co.uk] > I am looking into branching out into the contract research field. However, I am unsure of the average fees charged for such services, as I am from an academic research background. > > The various companies that offer this service do not publish their fee structures. I am sure quotes are given on a per contract basis, but there has to be a guiding hourly/daily rate which can be used for quoting. > > Thank you for your help.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Dec 15 09:59:00 2010 From: "Adam Sykes admin**quanano.co.uk" To: CCL Subject: CCL: Average Computational Chemistry Contract Research Fees Message-Id: <-43394-101215042547-18684-btwG2ZYQ1cazFIAFesY5Bg:-:server.ccl.net> X-Original-From: Adam Sykes Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 Dec 2010 09:25:30 -0000 MIME-Version: 1.0 Sent to CCL by: Adam Sykes [admin]^[quanano.co.uk] Thank you for your advice, that sounds like a good plan. Whilst I do not have experience contracting in computational chemistry; I have run my own IT consultancy for the past 3 years. So, I am OK with the running a business and dealing with clients, but you are correct in that there will have be some serious networking to do. Best wishes, Adam Dr. Adam Sykes MChem., PhD. Managing Director QuaNano Ltd e: adam.sykes/a\quanano.co.uk m: +44 (0)7855 379 397 t: +44 (0)151 324 2866 w: http://www.quanano.co.uk -----Original Message----- > From: owner-chemistry+adam.sykes==quanano.co.uk/a\ccl.net [mailto:owner-chemistry+adam.sykes==quanano.co.uk/a\ccl.net] On Behalf Of Vincent Leroux vincent.leroux%x%loria.fr Sent: 14 December 2010 21:37 To: Sykes, Adam C Subject: CCL: Average Computational Chemistry Contract Research Fees Sent to CCL by: Vincent Leroux [vincent.leroux%x%loria.fr] Tips from an academic who did not yet come to see if the pastures are greener on the other side of the fence (and feeling very uncertain about that, despite currently running out of grass) - for what it is worth You should go to the next big conference and picture yourself as a representative for some company to the stands - not here for signing something big right know, but to check the temperature before reporting to the heads. If you bring some example cases of "things we are considering right now", I guess the Chindian companies will easily give you the median prices as a first proposal. As this is all contract-based, I suppose that in many cases there is no such thing as daily rates - rather more or less stringent deadlines that will influence the price of the whole package. If there are some highly-demanding computations involved, this is another big factor... In any case, the amount of work you will do is nothing - this is all related to the cost of things done internally compared to what you ask for to get the job done... you have to be cheaper, but not too much, or you might not be taken seriously even with some solid references. In addition, you would also have the opportunity to discuss with your possible future clients - feel free to present yourself as an academic then, just curious about things are working on the dark side with all this externalization going on. You might be discouraged by how many possible future clients turn all of a sudden into possible future competitors ;-) In any case, you should have some kind of network in the industry already, or at least know some academics that went there and could provide you with more detailed information. You seem pretty courageous, as to plan turning into a contractor without much experience! Good luck. VL Le 14/12/10 17:16, A C Sykes adam.sykes^_^quanano.co.uk a écrit : > Sent to CCL by: "A C Sykes" [adam.sykes(_)quanano.co.uk] > I am looking into branching out into the contract research field. However, I am unsure of the average fees charged for such services, as I am from an academic research background. > > The various companies that offer this service do not publish their fee structures. I am sure quotes are given on a per contract basis, but there has to be a guiding hourly/daily rate which can be used for quoting. > > Thank you for your help.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Dec 15 10:34:00 2010 From: "=?utf-8?q?=C3=96d=C3=B6n_Farkas?= farkas]^[chem.elte.hu" To: CCL Subject: CCL: Schematic optimization sequence Message-Id: <-43395-101215052829-4566-ZcCfd+e19qbI/+1hoCwKaA^^^server.ccl.net> X-Original-From: =?utf-8?q?=C3=96d=C3=B6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 15 Dec 2010 11:28:07 +0100 MIME-Version: 1.0 Sent to CCL by: =?utf-8?q?=C3=96d=C3=B6n_Farkas?= [farkas^^^chem.elte.hu] Hi Peter, People (and it seems zou also) mix the geometry optimization and constructing the wavefunction for the molecule. Finding the appropriate wavefunction is many times a variational problem, therefore itself contains some sort of optimization. However, what you refer to as Berny optimization (Named after its "father" prof. H. Bernhard Schlegel) is geometry optimization and its goal to find a stationary point on the potential energy (hyper)surface, which is defined by the wavefunction and the total energy of the system. You can find his papers on his webpage: http://www.chem.wayne.edu/schlegel/Current/Schlegel.html Unfortunately, other than the geometry optimization uses the gradient (first derivative of the energy with respect to atomic coordinates) and then predicts iteratively the position of the critical point until convergence (based on gradient and step size based limits) cannot be said on non-mathematical way about the process. If you have problems about the math involved I can help you but I cannot really gide you without involving at least some of the math concerned. I hope I could help. Best wishes, Ă–dön Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány PĂ©ter sĂ©tány H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Monday 13 December 2010 13:28:37 P.D.Jarowski##surrey.ac.uk wrote: > Hi, thanks to all for their helpful comments on previous posts! > > I would like to know if there are any online sources out there that > describe in a didactic non-mathematical way how various computational ab > initio sequences are caried out. Especially, for multireference methods. > For example, what exactly in Berney optimization and how does is work > within the scf procedure? I would love to have such a source for my > students. > > Thanks, > > Best, > > Peter > ***Sent via RoadSync® for Android™ From owner-chemistry@ccl.net Wed Dec 15 11:09:00 2010 From: "=?utf-8?q?=C3=96d=C3=B6n_Farkas?= farkas]![chem.elte.hu" To: CCL Subject: CCL:G: Schematic optimization sequence Message-Id: <-43396-101215080935-26166-mGxOsTPz1RnGPsTmPNHP9g##server.ccl.net> X-Original-From: =?utf-8?q?=C3=96d=C3=B6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 15 Dec 2010 14:09:07 +0100 MIME-Version: 1.0 Sent to CCL by: =?utf-8?q?=C3=96d=C3=B6n_Farkas?= [farkas ~~ chem.elte.hu] Hi Peter, People (and it seems you also) sometimes mix the geometry optimization and constructing the wavefunction for the molecule. Finding the appropriate wavefunction is many times a variational problem, therefore itself contains some sort of optimization. However, what you refer to as Berny optimization (Named after its "father", prof. H. Bernhard Schlegel) is geometry optimization and its goal to find a stationary point on the potential energy (hyper)surface, which is defined by the wavefunction and the total energy of the system. You can find his papers on his webpage: http://www.chem.wayne.edu/schlegel/Current/Schlegel.html You may also follow the references in the chapter for the "Opt" keyword in the Gaussian manual, which is available online at www.gaussian.com. Unfortunately, other than that the geometry optimization uses the gradient (first derivative of the energy with respect to atomic coordinates) and then predicts iteratively the position of the critical point until convergence (using gradient and step size based limits) cannot be said on non-mathematical way about the process. If you have problems about the math involved I can help you but I cannot really gide you without involving at least some of the math concerned. I hope I could help. Best wishes, Ă–dön Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány PĂ©ter sĂ©tány H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Monday 13 December 2010 13:28:37 P.D.Jarowski##surrey.ac.uk wrote: > Hi, thanks to all for their helpful comments on previous posts! > > I would like to know if there are any online sources out there that > describe in a didactic non-mathematical way how various computational ab > initio sequences are caried out. Especially, for multireference methods. > For example, what exactly in Berney optimization and how does is work > within the scf procedure? I would love to have such a source for my > students. > > Thanks, > > Best, > > Peter > ***Sent via RoadSync® for Android™ From owner-chemistry@ccl.net Wed Dec 15 11:44:00 2010 From: "Adam Sykes admin!=!quanano.co.uk" To: CCL Subject: CCL: Average Computational Chemistry Contract Research Fees Message-Id: <-43397-101215105542-22027-dMdfNmI/oQl/rLPGlQw1eg~!~server.ccl.net> X-Original-From: Adam Sykes Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 Dec 2010 15:56:13 -0000 MIME-Version: 1.0 Sent to CCL by: Adam Sykes [admin%x%quanano.co.uk] Dear All, I would like to offer a big thank you to all that helped with this question. I am very grateful for your advice. Best wishes, Adam Dr. Adam Sykes MChem., PhD. Managing Director QuaNano Ltd e: adam.sykes]_[quanano.co.uk m: +44 (0)7855 379 397 t: +44 (0)151 324 2866 w: http://www.quanano.co.uk -----Original Message----- > From: owner-chemistry+adam.sykes==quanano.co.uk]_[ccl.net [mailto:owner-chemistry+adam.sykes==quanano.co.uk]_[ccl.net] On Behalf Of A C Sykes adam.sykes^_^quanano.co.uk Sent: 14 December 2010 16:16 To: Sykes, Adam C Subject: CCL: Average Computational Chemistry Contract Research Fees Sent to CCL by: "A C Sykes" [adam.sykes(_)quanano.co.uk] I am looking into branching out into the contract research field. However, I am unsure of the average fees charged for such services, as I am from an academic research background. The various companies that offer this service do not publish their fee structures. I am sure quotes are given on a per contract basis, but there has to be a guiding hourly/daily rate which can be used for quoting. Thank you for your help.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Dec 15 12:27:00 2010 From: "Wendy Anne Warr wendy:-:warr.com" To: CCL Subject: CCL: Multimedia and Visualization Innovations for Science Message-Id: <-43398-101215092820-6989-RXINqWe0yeRuXOngZuUwVw=server.ccl.net> X-Original-From: "Wendy Anne Warr" Date: Wed, 15 Dec 2010 09:28:17 -0500 Sent to CCL by: "Wendy Anne Warr" [wendy|*|warr.com] 8 FEBRUARY 2011 Multimedia and Visualization Innovations for Science A One-Day Workshop hosted by Microsoft Venue Microsoft Research, One Microsoft Way, Building 99, Redmond, WA 98502, USA Tuesday 8 February 2011 - 9.00am to 5.30pm (Check-in and breakfast from 8.15am) Why attend Multimedia and visualization tools and technology offer tremendous opportunity for accelerating scientific discovery. Where science was once limited to text and two-dimensional graphs and charts for communications purposes, multiple factors have contributed to a rise in the use and availability of multimedia and visualization as tools to augment and enhance more rapid uptake of science. This workshop will feature leading-edge innovations in science-oriented web multimedia, large-scale data exploration and visualization, speech and object recognition, image indexing and analysis, human/computer interaction and virtual environments, among other topics. Presentations will be made by technology, science, and information professionals across the broad spectrum of academia, government, business, and industry. Confirmed Speakers and Topics * Peter Tu, GE Global Research, "Video Analytics and its Application to Science and Technology." * Behrooz Chitsaz, Microsoft Research, and Lorrie Apple Johnson, U.S. Department of Energy Office of Scientific and Technical Information, "ScienceCinema: Multimedia Search and Retrieval in the Sciences." * Wilmot Li, Adobe Systems, "Explaining Complex 3D Objects with Interactive Illustrations." * Tim Smith, CERN (The European Organization for Nuclear Research), "Communications from the Particle Frontier." * Michael Ackerman, National Library of Medicine, "Interactive Multimedia Scientific Publishing." * Alexander Waibel, Carnegie Mellon University, "Speech Processing Applications in Quaero (European Multimedia Search Engine)." * Robert M. Hanson, St. Olaf College, "Delivering Interactive 3D Molecular Structure - The Jmol Solution." * Rafael Sidi, Elsevier, "The Impact of Visualization on Search and Discovery" * Curtis Wong, Microsoft Research, "Telling Stories in the Cloud" * Peter Fox, Tetherless World Constellation, Rensselaer Polytechnic Institute, "Semantics for Innovation in Visualization and Multimedia; Smarter Information Science." * Jennifer Lin, Microsoft Corporation, "PivotViewer: A Living Infographic for Your Data." * Mike Frame, U.S. Geological Survey, "Visualization and Indexing of Ecological/Biological Data." REGISTRATION OPEN FROM NOVEMBER 2, 2010 Registration: Because seats are limited, advance registration is required. The registration fee, which includes continental breakfast, lunch and refreshment breaks, is $250/295 (before/after 5 January) for ICSTI members, $300/395 (before/after 5 January) for non-members and $150/195 (before/after 5 January) for students. Members of ALPSP, NFAIS, GreyNet, and CENDI are eligible for the member rate for this event, as are members of ICSU's scientific unions and CODATA. Check the ICSTI website URL http://www.icsti.org/ for updates, including additional speakers, final program content and registration form. *****************************************************************************************************************For more information, contact the organizers Brian Hitson, US Department of Energy, hitsonb|*|osti.gov, Tony Llewellyn, ICSTI Executive Director, aj.llewellyn|*|btinternet.com, or the ICSTI Secretariat. ICSTI Secretariat: 33, rue de Naples - 75008 Paris - France Email : icsti|*|voila.fr Tel: +33 (0)6 14 65 16 57 From owner-chemistry@ccl.net Wed Dec 15 13:55:01 2010 From: "Jamin Krinsky krinsky.jamin%a%gmail.com" To: CCL Subject: CCL: Queries on TDDFT calculations on emission Message-Id: <-43399-101215135031-25109-AwP2KVe/uAAM4OonLZGooA#,#server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 Dec 2010 10:50:01 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [krinsky.jamin]=[gmail.com] Dear Eliz, It depends on which type of emission you want to model. Absorption will normally be only from the ground singlet state to various excited singlet states. Fluorescence occurs from the lowest singlet excited state to the ground state, but at the geometry of the first singlet excited state. So you would need to do a TDDFT optimization at the first singlet excited state, and the emission wavelength would be the excitation energy at the end of your optimization. If inter-system crossing can occur, the first singlet excited state can relax to the first triplet excited state. Because emission from this state to the ground state is spin forbidden the excited state will be longer-lived, and the emission process is phosphorescence. The cheapest (and pretty reasonable) way to calculate that emission is to do a geometry optimization on the "ground state" triplet using unrestricted, normal DFT, then do a TDDFT calculation from the singlet at that geometry and specify triplet excited states. Note that this last calculation will not give you oscillator strengths, just wavelengths. This basic discussion can be found in any good comp. chem. text, but if you are just starting out you should read up on when you can believe your results, for example: J. Chem. Phys. 2002, 117, 5543 J. Am. Chem. Soc. 2004, 126, 4007 J. Chem. Phys. 2008, 128, 044118 Other people might have some better references for these things, this is just what I happen to have in front of me. Good luck, Jamin On Wed, Dec 15, 2010 at 2:45 AM, Eliz Lam elizabeth.shlam:_:gmail.com wrote: > > Sent to CCL by: "Eliz  Lam" [elizabeth.shlam*|*gmail.com] > Dear CCLers, > > Hi, I'm a beginner in learning DFT and TDDFT calculations and have some queries on calculating emission properties of a molecule.  I originally thought the emission of a molecule should be the first triplet excited state from TDDFT calculations as stated from Kasha's rule that the emissive state should be of the lowest energy.  However, it seems not always the case.  I'm wondering why one could not predict emission from the above way and how should one predict the emission of a molecule?  And is the emission mechanism originated the same as from first triplet excited state in the TDDFT calculations? > > Thank you so much! > Eliz>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Wed Dec 15 14:30:00 2010 From: "Van Dam, Hubertus J HubertusJJ.vanDam:_:pnl.gov" To: CCL Subject: CCL: Queries on TDDFT calculations on emission Message-Id: <-43400-101215135955-29453-0B7SEJk1dKW583tj4x3G4g*server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 15 Dec 2010 10:59:04 -0800 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam]*[pnl.gov] Hi Eliz, I am not an expert on this topic, but your choice of the triplet excited state seems a bit strange. The transition between the singlet ground state and triplet excited state (assuming your molecule is a closed shell system) is spin forbidden. Hence the probability of such a transition occurring is very small (zero to be precise). You would probably need rovibronic couplings to be able to get any intensity at all. Therefore I would suggest that you look at the lowest excited singlet state instead and see if that makes more sense. Best wishes, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnl.gov#%#ccl.net [mailto:owner-chemistry+hubertus.vandam==pnl.gov#%#ccl.net] On Behalf Of Eliz Lam elizabeth.shlam:_:gmail.com Sent: Wednesday, December 15, 2010 2:45 AM To: Van Dam, Hubertus J Subject: CCL: Queries on TDDFT calculations on emission Sent to CCL by: "Eliz Lam" [elizabeth.shlam*|*gmail.com] Dear CCLers, Hi, I'm a beginner in learning DFT and TDDFT calculations and have some queries on calculating emission properties of a molecule. I originally thought the emission of a molecule should be the first triplet excited state from TDDFT calculations as stated from Kasha's rule that the emissive state should be of the lowest energy. However, it seems not always the case. I'm wondering why one could not predict emission from the above way and how should one predict the emission of a molecule? And is the emission mechanism originated the same as from first triplet excited state in the TDDFT calculations? Thank you so much! Elizhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Dec 15 16:25:00 2010 From: "Roy Jensen JensenRH/./MacEwan.ca" To: CCL Subject: CCL:G: geometry optimization of O2 (singlet delta) Message-Id: <-43401-101215154313-31606-hrJfS4OT0wkWD5OexxznUA*_*server.ccl.net> X-Original-From: Roy Jensen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 Dec 2010 13:43:12 -0700 MIME-Version: 1.0 Sent to CCL by: Roy Jensen [JensenRH{=}MacEwan.ca] I found that G03 Test Job 001 calculates the singlet delta energy of oxygen at fixed geometry. ******************** #P HF/STO-3G COMPLEX Gaussian Test Job 01 GROUND STATE STO-3G//STO-3G DIOXYGEN 0 1 O O 1 R R 1.22 ******************** Whereas removing the 'COMPLEX' keyword calculates the singlet sigma state. However, every time I attempt to do a geometry optimization, with both OPT and COMPLEX, it crashes. ******************** (Enter C:\G03W\l401.exe) Initial guess read from the read-write file: Guess basis will be translated and rotated to current coordinates. Unable to project occupied orbitals ! Error termination via Lnk1e in C:\G03W\l401.exe at Mon Dec 13 11:23:37 2010. ******************** According to the Gaussian manual, the COMPLEX keyword is very limiting. Is there another way to optimized to the singlet delta state of oxygen and oxygen analogues (NF specifically)? Thanks, Dr. Roy Jensen (==========)-----------------------------------------¤ Chemistry, Grant MacEwan University Room 5-172J, 10700-104 Avenue Edmonton, AB T5J 4S2 780.633.3915 From owner-chemistry@ccl.net Wed Dec 15 17:00:00 2010 From: "Serghei Glinca glinca(a)staff.uni-marburg.de" To: CCL Subject: CCL: H-bonding protein-ligand complexes Message-Id: <-43402-101215163116-10451-5bfWgs+2+qaXZkfLGqB96A===server.ccl.net> X-Original-From: Serghei Glinca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 15 Dec 2010 22:30:53 +0100 MIME-Version: 1.0 Sent to CCL by: Serghei Glinca [glinca-,-staff.uni-marburg.de] Dear Mohammad, I found following publication very helpful for the analysis of screening results regarding interactions discussed in the paper. "A Medicinal Chemist’s Guide to Molecular Interactions" from the group of Martin Stahl. Cheers, Serghei On 15/12/10 10:26, Mohammad Ghattas mah.ghattas,googlemail.com wrote: > Sent to CCL by: "Mohammad Ghattas" [mah.ghattas=googlemail.com] > Dear All, > > I've got many ligand-protein complexes to analyse but I'm not sure about the H- > bond range for a heavy atom to a heavy atom H-bonding as well as hydrogen to a > heavy atom H-bonding? and which is always better to consider in publications? > > Also, is anybody aware of a good paper discusses such topics, including other > possible types of interactions in ligand binding (hydrophobic and stacking > interactions)? > > Very best regards, > Mohammad> > -- Serghei Glinca Group of Prof. Dr. G. Klebe Department of Pharmaceutical Chemistry University of Marburg Marbacher Weg 6 D-35032 Marburg, Germany Phone: +49 6421 28-21339 Email: serghei.glinca ~ staff.uni-marburg.de www.agklebe.de From owner-chemistry@ccl.net Wed Dec 15 23:27:00 2010 From: "Jonathan Moore jonmower]^[gmail.com" To: CCL Subject: CCL: Results of the 6th Industrial Fluid Properties Simulation Challenge Message-Id: <-43403-101215164526-32073-Ytz3GRI2Ym72BIdTWzF8qg(_)server.ccl.net> X-Original-From: Jonathan Moore Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Wed, 15 Dec 2010 16:44:58 -0500 MIME-Version: 1.0 Sent to CCL by: Jonathan Moore [jonmower^^gmail.com] The results of the Sixth Industrial Fluid Properties Simulation Challenge were announced at a special session at the AIChE Annual Meeting in Salt Lake City in November 2010. Entrants were challenged to predict the mutual solubility in liquid-liquid equilibria of water and a glycol ether (PROGLYDE DMM *) as a function of temperature. Unlike most organic solvents, glycol ethers and glycol diethers exhibit an “inverse solubility” relationship with water. They are used in a wide range of product formulations and industrial processes. For example, they are used as solvents and co-solvents in both organic- and water-based formulations for applications such as cleaning solutions, paints, coatings, and inks. A variety of other novel applications have been proposed that take advantage of the inverse solubility behavior. Seven entries were received, and they were judged based on comparison to experimental data provided by The Dow Chemical Company. Five of the seven presented there results at the AIChE session before the announcement of the champions. J. Reinisch, A. Klamt, F. Eckert and M.Diedenhofen (COSMOlogic) were named Champions. P. Bai and J.I. Siepmann (U. Minnesota) were named Runners-Up. S.-T. Lin, L.-H. Wang, W.-L. Chen, P.-K. Lai, and C.-M. Hsieh (National Taiwan University) were named Honorable Mention. The other four entries were honored for participating: T. Koddermann, K. N. Kirschner, J. Vrabec, M. Hulsmann, D. Reith (SCAI; U. Paderborn); A. Vahid , F. S. Emami , E. Moharreri, J. R. Elliott (U. Akron); T. Cheng, F. Li, J. Dai, and H. Sun (Shanghai Jiao Tong University); and L. Zhao, C. Wub, and N. Huang (National Institute of Biological Sciences, Beijing, China; Washington University). Thanks to all who participated in planning and judging the challenge and to the entrants! It is anticipated that a 7th challenge will be planned for 2011. More info about the 6th Challenge and previous challenges can be found here: http://fluidproperties.org/simulation-challenge * - Trademark of The Dow Chemical Company