From owner-chemistry@ccl.net Tue Jan 16 09:05:00 2007 From: "debjani roy debjani_2k2 a yahoo.com" To: CCL Subject: CCL: VDW PARAMETER CONVERSION Message-Id: <-33377-070116043858-4931-VNC8NBRcYCNG1/5h8oTS9w:-:server.ccl.net> X-Original-From: "debjani roy" Date: Tue, 16 Jan 2007 04:38:54 -0500 Sent to CCL by: "debjani roy" [debjani_2k2 .. yahoo.com] Hi, I am looking for the MM2 to Amber conversion factor for VDW parameter. Thanks for your help in advance, From owner-chemistry@ccl.net Tue Jan 16 11:13:01 2007 From: "Aniko Simon aniko^simbiosys.ca" To: CCL Subject: CCL: new product: ARChem Route Designer v 1.1 from SimBioSys Message-Id: <-33378-070116111145-27629-NXACPGNVAmxstGhXBYAG3w-#-server.ccl.net> X-Original-From: "Aniko Simon" Date: Tue, 16 Jan 2007 11:11:41 -0500 Sent to CCL by: "Aniko Simon" [aniko-*-simbiosys.ca] SimBioSys is pleased to announce a new product: ARChem Route Designer ARChem Route Designer is an automatic retrosynthetic analysis tool for organic chemistry. Building on the success of the synthetic accessibility estimator, CAESA, SimBioSys has worked with Pfizer Inc., to develop the latest advancement in Computer Aided Organic Synthesis Design (CAOSD). ARChem Route Designer has a user-friendly web-based user interface for entering queries and viewing the resulting suggested routes. With enterprise level support, the system is designed to permit simultaneous use by hundreds of chemists. The unique interface allows the user to walk through the exhaustive solution tree to find the best retrosynthetic route possible. In an important departure from earlier retrosynthetic analysis systems, ARChem Route Designer incorporates an automated rule extraction engine to generate the retrosynthetic rules used in the analysis. This rule extraction engine takes literature-based reaction databases (in RD format, for example MOS from Accelrys) and automatically clusters together examples of specific reactions and then extracts the required chemical features to form a set of chemical rules that can be applied during retrosynthetic analysis. Try ARChem for yourself! ARChem Route Designer is now available for online demonstration. Simply fill out a "Request a Free Demo" form on our website and an account will be sent to you which will allow you to run retrosynthetic searches on your target molecules. For more information about ARChem, please visit: http://www.simbiosys.ca/archem/ Best regards, Aniko -- Aniko Simon SimBioSys Inc. tel: 416-741-4263 http://www.simbiosys.ca/ From owner-chemistry@ccl.net Tue Jan 16 12:27:01 2007 From: "Andrew Orry andy()molsoft.com" To: CCL Subject: CCL: chemical database software Message-Id: <-33379-070115215151-19853-bvNxekP5mXUoFpr+u4/7vQ=-=server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 15 Jan 2007 17:57:21 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy^molsoft.com] Martin Mueller martin.mueller++ime.fraunhofer.de wrote: > > Sent to CCL by: Martin Mueller [martin.mueller===ime.fraunhofer.de] > Hi, > > I'm looking for database software (commercial or free) for storage of > chemical structures and related data (something like MDL Direct) > Please see MolCart (http://www.molsoft.com/molcart.html) and MolCart Compounds (http://www.molsoft.com/molcart-compounds.html). Thanks, Andy -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com From owner-chemistry@ccl.net Tue Jan 16 15:35:00 2007 From: "Satyan Sharma satyan+/-sun3.oulu.fi" To: CCL Subject: CCL: Gaussian QST2 Message-Id: <-33380-070116144546-24338-Lh9yi+piO4Sj3vi0u1VM3w]^[server.ccl.net> X-Original-From: Satyan Sharma Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 16 Jan 2007 20:57:15 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Satyan Sharma [satyan:_:sun3.oulu.fi] Hello everybody, I am trying to do TS search using following route: #N B3LYP/GEN OPT=QST2 Nosymm TEST Optimization went fine for 8 steps. In the 8th step I see this: Step number 8 out of a maximum of 510 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using D2CorX and points 5 6 7 8 Eigenvalues --- -0.00335 0.00229 0.00230 0.00232 0.00233 Eigenvalues --- 0.00250 0.00293 0.00330 0.00377 0.00486 Eigenvalues --- 0.00555 0.00584 0.00706 0.00930 0.00989 But in the 9th step : Step number 9 out of a maximum of 510 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using D2CorX and points 8 9 Eigenvalues --- ********** 0.04188 0.04803 0.06493 0.06961 Eigenvalues --- 0.08716 0.09281 0.11078 0.11260 0.13017 And the run stopped with following message: 544 D251 0.00079 0.00079 -49.92858********** 545 D252 0.00000 0.00000 -45.00426********** 546 D253 0.00103 0.00103 -0.00008 0.00816 RFO step: Lambda0=3.127208390D+13 Lambda=-8.54305189D-03. Arithmetic Exception Please let me know if you have an idea. Cheers, Satyan Sharma From owner-chemistry@ccl.net Tue Jan 16 17:28:00 2007 From: "Dr. Seth Olsen s.olsen1{=}uq.edu.au" To: CCL Subject: CCL: Photoexcited states from time dependent DFT Message-Id: <-33381-070115181909-3670-egZt7QSKu18nkgup2XZMNw:+:server.ccl.net> X-Original-From: "Dr. Seth Olsen" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 16 Jan 2007 08:31:38 +1000 MIME-Version: 1.0 Sent to CCL by: "Dr. Seth Olsen" [s.olsen1#%#uq.edu.au] Hi Andrew, The short answer to your question is that usual implementations of TDDFT are constrained by problems similar to those found with Configuration Interaction Singles (CIS). Most implementations of TDDFT are of 'linear response' type. CIS is generally considered to be a single-determinant excited state method (i.e. excited states can be written as single determinants within the method, the excitations being to first order equivalent with orbital rotations). Linear response TDDFT often does better with excitation energies than CIS, though I do not know enough to tell you why (probably cancellation of error, and it depends on the functional). TDDFT is known to have problems with excited states involving 'long-range' charge transfer, in which case excitation energies are severly underestimated. The reasons for this pathology are buried in the approximations made in creating a 'local' functional. If you can, I would test your TDDFT results using small models of your polymer by comparing against CASPT2 (or, if possible EOM-CCSD with a modest basis) in order to make sure that TDDFT can handle the states you are interested in. There are some implementations of TDDFT that are not linear response methods (I think OCTOPUS is one of these). I _THINK_ that these may be able to capture some of the multi-configuration character you allude to, but I don't know enough to say. Results in the literature that I have seen are somewhat promising. These may be more time-intensive because they integrate the density in real time. Your concerns are well placed, and the shortcomings which you allude to become quite pathological in the region around intersections between states. See Levine, Ko, Quenneville & Martinez, Mol. Phys. 104 pp.1039-1051 (2006). Cheers, Seth Van Dam, HJJ (Huub) h.j.j.vandam() dl.ac.uk wrote: >Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam:_:dl.ac.uk] >Hi Andrew, > >Very recently a new book on TDDFT has appeared. I have just got it from >the library and it certainly looks very impressive. It covers almost >everything from the formal foundations of TDDFT to applications. The >answer to your question will most certainly be in there. The reference >is: > >M.A.L. Marques, A. Rubio, C.A. Ullrich, K. Burke, F. Nogueira, E.K.U. >Gross >"Time Dependent Density Functional Theory" >Lecture Notes In Physics 706 >Springer, Berlin Heidelberg, 2006 >DOI:10.1007/b11767107 >ISBN-10 3-540-35422-0 >ISBN-13 978-3-540-35422-2 > >I hope this helps. > >Best wishes, > > Huub > > >========================================================== >Huub van Dam (h.j.j.vandam(~)dl.ac.uk, +44-1925-603933) >========================================================== > > >-----Original Message----- > > >>From: owner-chemistry(~)ccl.net [mailto:owner-chemistry(~)ccl.net] >> >> >Sent: 10 January 2007 15:12 >To: Vandam, Huub >Subject: CCL: Photoexcited states from time dependent DFT > > >Sent to CCL by: Andrew Horsfield [a.horsfield:ucl.ac.uk] > >Hi, > >I am studying a strand of photoexcited polymer using a simple electronic >structure model, but would like to improve on this by using DFT. I >believe that TDDFT is the correct theory for obtaining excited states. >However, there is one question that troubles me. > >The ground state is a spin singlet. Thus photoexcitation takes us to >excited states that are also spin singlets. Now, in general more than >one slater determinant is needed to describe an excited spin singlet >state, while Kohn-Sham DFT works with just one determinant. So how does >TDDFT describe these states? > >I would welcome a reference to a good TDDFT review article or book. > >Cheers, > >Andrew > > > -- ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Australian Institute For Bioengineering and Nanotechnology (75) The University of Queensland Brisbane Qld 4072 Australia Tel: +61 7 3346 3946 Fax: +61 7 3346 3992 email: s.olsen1- -uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland From owner-chemistry@ccl.net Tue Jan 16 18:02:00 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas*chem.elte.hu" To: CCL Subject: CCL:G: Gaussian QST2 Message-Id: <-33382-070116163449-19606-z8IrXOTAUBlwVEMiamJnNQ(_)server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 16 Jan 2007 22:33:45 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas ~~ chem.elte.hu] Hi Satyan, This is very likely related to an internal coordinate system problem, Try creating a QST3 input using the starting geometry and the one from step #8. For this kind of input G03 will create redundant internals which are valid for all three structures. Best wishes, Odon On Tue, 2007-01-16 at 20:57 +0200, Satyan Sharma satyan+/-sun3.oulu.fi wrote: > Sent to CCL by: Satyan Sharma [satyan:_:sun3.oulu.fi] > Hello everybody, > I am trying to do TS search using following route: > > #N B3LYP/GEN OPT=QST2 Nosymm TEST > > Optimization went fine for 8 steps. In the 8th step I see this: > Step number 8 out of a maximum of 510 > All quantities printed in internal units (Hartrees-Bohrs-Radians) > Update second derivatives using D2CorX and points 5 6 7 8 > Eigenvalues --- -0.00335 0.00229 0.00230 0.00232 0.00233 > Eigenvalues --- 0.00250 0.00293 0.00330 0.00377 0.00486 > Eigenvalues --- 0.00555 0.00584 0.00706 0.00930 0.00989 > > But in the 9th step : > Step number 9 out of a maximum of 510 > All quantities printed in internal units (Hartrees-Bohrs-Radians) > Update second derivatives using D2CorX and points 8 9 > Eigenvalues --- ********** 0.04188 0.04803 0.06493 0.06961 > Eigenvalues --- 0.08716 0.09281 0.11078 0.11260 0.13017 > > And the run stopped with following message: > 544 D251 0.00079 0.00079 -49.92858********** > 545 D252 0.00000 0.00000 -45.00426********** > 546 D253 0.00103 0.00103 -0.00008 0.00816 > RFO step: Lambda0=3.127208390D+13 Lambda=-8.54305189D-03. > Arithmetic Exception > > Please let me know if you have an idea. > Cheers, > Satyan Sharma> > > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Tue Jan 16 18:37:00 2007 From: "Shobe, David David.Shobe^^sud-chemie.com" To: CCL Subject: CCL:G: Gaussian QST2 Message-Id: <-33383-070116163435-19558-Vd4FZmAF9v3BJ6giGEpnSg::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, 16 Jan 2007 22:25:12 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe**sud-chemie.com] If possible, restart the calculation at the geometry of step 8 (or maybe step 7), using the calcfc option. Either your optimization took a giant "step" to a very different geometry, or your molecule has transitioned to another electronic state. Regards, --David Shobe Süd-Chemie, Inc. Attention to detial is essentail. -----Original Message----- > From: owner-chemistry:_:ccl.net [mailto:owner-chemistry:_:ccl.net] Sent: Tuesday, January 16, 2007 1:57 PM To: Shobe, David Subject: CCL: Gaussian QST2 Sent to CCL by: Satyan Sharma [satyan:_:sun3.oulu.fi] Hello everybody, I am trying to do TS search using following route: #N B3LYP/GEN OPT=QST2 Nosymm TEST Optimization went fine for 8 steps. In the 8th step I see this: Step number 8 out of a maximum of 510 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using D2CorX and points 5 6 7 8 Eigenvalues --- -0.00335 0.00229 0.00230 0.00232 0.00233 Eigenvalues --- 0.00250 0.00293 0.00330 0.00377 0.00486 Eigenvalues --- 0.00555 0.00584 0.00706 0.00930 0.00989 But in the 9th step : Step number 9 out of a maximum of 510 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using D2CorX and points 8 9 Eigenvalues --- ********** 0.04188 0.04803 0.06493 0.06961 Eigenvalues --- 0.08716 0.09281 0.11078 0.11260 0.13017 And the run stopped with following message: 544 D251 0.00079 0.00079 -49.92858********** 545 D252 0.00000 0.00000 -45.00426********** 546 D253 0.00103 0.00103 -0.00008 0.00816 RFO step: Lambda0=3.127208390D+13 Lambda=-8.54305189D-03. Arithmetic Exception Please let me know if you have an idea. Cheers, Satyan Sharmahttp://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 Jan 16 22:54:00 2007 From: "Andrew D. Fant fant-x-pobox.com" To: CCL Subject: CCL: chemical database software Message-Id: <-33384-070116224315-8951-Jvh4dLCZ2f9MUBYQXu6POw()server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 16 Jan 2007 22:43:02 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant+/-pobox.com] Martin Mueller martin.mueller++ime.fraunhofer.de wrote: > > Sent to CCL by: Martin Mueller [martin.mueller===ime.fraunhofer.de] > Hi, > > I'm looking for database software (commercial or free) for storage of > chemical structures and related data (something like MDL Direct) > PGChem is an open-source extension to postgres for chemical structure data (http://pgfoundry.org/projects/pgchem/) I haven't done much with it, and you will probably need to code your own clients to meet your needs, but it certainly will do what you are asking. Alternately, if money is no object, there is always the Accord suite from Accelrys, which is, I believe, what RS3 mutated into. It's commercial and sits on top of Oracle ( or excel or access for smaller applications) and has all sorts of bells and whistles if you are doing this for an organization that wants batteries included and a vendor to flog if anything ever goes wrong. Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant-x-pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Tue Jan 16 23:28:01 2007 From: "Mike Towler mike_towler.[*].postmaster.co.uk" To: CCL Subject: CCL: QMC Summer School, Tuscany, July 2007 Message-Id: <-33385-070116210819-3154-UNz+KR17sMLIntVQnihedw[*]server.ccl.net> X-Original-From: "Mike Towler" Date: Tue, 16 Jan 2007 21:08:16 -0500 Sent to CCL by: "Mike Towler" [mike_towler-#-postmaster.co.uk] SUMMER SCHOOL ANNOUNCEMENT "Quantum Monte Carlo and the CASINO program II" =============================================== Sun 29th July - Sun 5th August 2007 The Towler Institute, 22 via del Collegio, Vallico Sotto, Tuscany, Italy http://www.tcm.phy.cam.ac.uk/~mdt26/tti/tti.html HI-RES POSTER FOR THE SCHOOL AVAILABLE HERE: http://www.tcm.phy.cam.ac.uk/~mdt26/tti/qmcatcp_07/tti.jpg The second international summer school in the series "Quantum Monte Carlo and the CASINO program" will take place in July/August 2007 at the Towler Institute monastery in the Tuscan Apuan Alps, organized and hosted by members of Cambridge University physics department's Theory of Condensed Matter (TCM) Group. The aim of the school is to give students a thorough introduction to quantum Monte Carlo as a method for performing highly accurate calculations of the electronic structure of real materials. The course is designed for young scientists who have no previous experience with this technique, though anyone interested is welcome to take part. Many-body quantum theory provides the key ideas for understanding the behaviour of materials at the level of the electrons which bind the atoms together. Describing the complex behaviour of materials at the atomic level requires a sophisticated description of the correlated motion of the electrons, which can be achieved using ab initio computational methods. Quantum Monte Carlo in particular has many attractive features in this regard. It is an explicitly many-body method which takes electron correlation into account from the outset, and is capable of giving highly accurate results while at the same time exhibiting a very favourable scaling of computational cost with system size. Over the last sixteen years, the Cambridge group have been researching QMC methods and we have created a powerful, general computer program - CASINO - to carry out the calculations. The school will focus both on the basic theory of QMC and on more advanced practical techniques, and will include a thorough introduction to the CASINO program. A background in density functional theory or similar is normally thought to be useful. The monastery is a delightful 16th century building incorporating an ancient church, and is situated in the isolated but spectacular setting of the Tuscan mountain village of Vallico Sotto. It is fully equipped with state of the art presentation and computer technology. All accommodation is on-site. There is a strictly-enforced policy for all events at the Institute that considerable time should be set aside for mountain hikes, caving, canyon walking, swimming in thermal baths, eating in wonderful local restaurants, visits to classical concerts in Lucca and Barga, and similar activities. It is to be hoped that the visitor will not mind this too much. Instructors will include the main authors of the CASINO program, (Prof. Richard Needs, Dr. Mike Towler, Dr. Neil Drummond, and Dr. Pablo Lopez Rios) and very probably others. The cost of the school for one week including accommodation will be around 400 GBP. Participants would need to arrange a flight to Pisa airport from where onward transportation will be arranged. Interested students should contact Mike Towler (mdt26 at cam.ac.uk) for registration and further details. Nice emails from students attending "QMC and the CASINO program" in 2006: ------------------------------------------------------------------------- "Just a brief note to thank you again for hosting the QMC summer school. I had a wonderful time in Tuscany, it was probably the best conference/school I've attended. The science was excellent, and the location, obviously, stunning. The Towler Institute is a very impressive place. Every one of the participants was a pleasure to spend time with, and I've come away with some friends with whom I intend to keep in contact." "Thank you so much, it was a great pleasure being at the school. The presentations were all very good and the place and people really nice." "Thanks for all, the school was really great, helpful and very well organized." "I will advice your school to anyone on the earth" DETAILS AND PHOTOS FROM LAST YEARS EVENT ACCESSIBLE ON TTI WEB PAGE. TTI CURRENTLY TAKING BOOKINGS FOR THE HOSTING OF CONFERENCES, SCHOOLS AND GROUP MEETINGS IN EASTER/SUMMER 2007. Enquiries to mdt26 at cam.ac.uk .