From owner-chemistry@ccl.net Thu Jul 12 00:14:00 2007 From: "neeraj misra misraneeraj.]*[.gmail.com" To: CCL Subject: CCL: ONIOM Message-Id: <-34732-070712001038-26114-Ar8y3x3jcImkGjYxGBxYag]*[server.ccl.net> X-Original-From: "neeraj misra" Date: Thu, 12 Jul 2007 00:10:33 -0400 Sent to CCL by: "neeraj misra" [misraneeraj[*]gmail.com] Dear CCL'ers, I am looking for some basics of ONOIM method. I need to partition a molecular system into different sheels and deal the inner shell with DFT (B3LYP)6-31G(d) and the outer shell with MP2(6-31G(d)).How to proceed for such type of calculation (using GO3).Any help would be greatfully acknowledged. nm From owner-chemistry@ccl.net Thu Jul 12 10:08:01 2007 From: "Yuan Zhao ccl|-|mail.sioc.ac.cn" To: CCL Subject: CCL: Where to find FDA drug database Message-Id: <-34733-070712100558-5016-QiPHl6i8lRhV5I1ZitH1pQ|,|server.ccl.net> X-Original-From: "Yuan Zhao" Date: Thu, 12 Jul 2007 10:05:55 -0400 Sent to CCL by: "Yuan Zhao" [ccl ~~ mail.sioc.ac.cn] Thanks! I've downloaded the database in DrugBank. It contains 1066 molecules in the sdf file, of which 11 are blank molecules and 10 contain '*' in atomic name. However, I searched in google and found a software named as "Synapse EMR Express SERVER" which seemed to be able to download and install FDA drug database. It imported about 21000 pieces of infomation but I could not find them. Does it mean that there are over 21000 drugs in FDA database? If it is the truth, the molecules in DrugBank seem too few to summarize the property of FDA database. Steven ======================================================================== CCL: Where to find FDA drug database Sent to CCL by: [DSprous*redpointbio.com] In reply to "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] query summarized as: "I wonder how many drugs FDA have approved till now or this year?" To my knowledge: The FDA Orange Book (http://www.fda.gov/cder/ob/) is closest publicly available answer to this question. It is a list of approved drug formulations and does not have structures. Further, since it is a list of approved formulations, children's motrin is distinct from adult strength which is different from extra strength. The FDA apparently simply does not seem to be interested in an actual molecular database of approved active ingredients. You would need to download a copy of the list, develop a script to generate a unique list of active ingredients and then use something like LexiChem to convert the chemical and trade names to SMILES. This gives one about 1300 to 1400 compounds. An alternative which is easier to work with is the DrugBank (http://redpoll.pharmacy.ualberta.ca/drugbank/) datasets maintained by Wishart [University of Alberta]. This too is a list of ~1300 to 1400 compounds. If anyone knows better public sources, please post. Dennis G. Sprous, PhD Chemoinformatics/Computational Chemistry RedPointBio Inc. 7 Graphics Drive Ewing NJ 08628 609-637-9700 -----Original Message----- > From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net] Sent: Wednesday, July 11, 2007 10:40 AM To: Dennis Sprous Subject: CCL: Where to find FDA drug database Sent to CCL by: "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] Hi all, I wonder how many drugs FDA have approved till now or this year. If possible, where can I download the FDA drug database in sd, mol or other chemical formats? Does anyone know how many drugs in FDA are fit for Lipinski rule of five? Any clue will be appreciate. Thanks. Stevenhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://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 Thu Jul 12 12:35:01 2007 From: "errol lewars elewars]*[trentu.ca" To: CCL Subject: CCL:G: Appropriateness of G3 (G3MP2) Theory for Vertical Ionization Energies Message-Id: <-34734-070712105500-31795-ntk3ZLaJCaLFDVX5zajMBA:_:server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 12 Jul 2007 10:55:13 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars- -trentu.ca] 2007 July 12 Intuitively, it seems reasonable to use the same ZPE for the ground and the vertically ionized state, i.e to omit the ZPE (since ZPE - ZPE = 0), since we want the energy it takes to go to the ionized state _before that species can do anything_. Pragmatically, though, one could compile a list of molecules and their experimental vertical IEs, and see which procedure gives the best match to experiment. E. Lewars === Soren Eustis soren_-_jhu.edu wrote: >Sent to CCL by: "Soren Eustis" [soren*|*jhu.edu] >Good post. I had a similar question regarding the use of zero point >corrections for adiabatic electron affinities and vertical electron >affinities. Clearly, the use of ZPE corrections for the adiabatic case is >needed. However for the vertical case it makes sense to use only the ZPE of >the initial state (in my case the anion), since the energy level being >accessed in the final state is indeed well above the ground state. > >However, I have found that for large molecules with significant degrees of >freedom, the ZPE of the initial state is so large as to make the vertical >energies very small. Thus, the calculation of vertical electron affinities >only work if I use the non-ZPE corrected values for the anion and the >neutral. This makes no chemical sense to me, but the numbers line up well >this way. > >For your case I would say that calculating frequencies of a species that is >not in a potential well is meaningless. I would suggest doing single point >energy calculations for both species and then doing separate frequency >calculations for the initial state. However, I am curious as to what the >ZPE will do to your IP values. > >Anyone have any thoughts on this. It seems common in the literature that >ZPE's are used for adiabatic calculations only, and they are completely >ignored (even for the initial state) for vertical calculations. This seems >to line up with experiment, but it is unsatisfying intellectually. > >Soren N. Eustis >Graduate Research Assistant >Department of Chemistry >Johns Hopkins University >Remsen Hall >3400 N Charles Street >Baltimore, MD 21218 >(410) 516-4675 (office) >(410) 925-5167 (cell) >(410) 516-8420 (fax) >soren!=!jhu.edu >-----Original Message----- > > >>From: owner-chemistry!=!ccl.net [mailto:owner-chemistry!=!ccl.net] >> >> >Sent: Tuesday, July 10, 2007 10:56 AM >To: Eustis, Soren >Subject: CCL:G: Appropriateness of G3 (G3MP2) Theory for Vertical Ionization >Energies > > >Sent to CCL by: "Abrash, Samuel" [sabrash~!~richmond.edu] >Hi Folks, > >I have a question about both the appropriateness of G3MP2 for calculating >vertical ionization energies, and in addition for the use of G03 frequency >calculations for calculating zero point corrections for the ion in a >vertical ionization energy calculation. Here are the details. > >I'm doing a series of calculations on adiabatic and vertical ionization >energies of isomers of C6H6. I'd like to do them at both the >UPBEPBE/aug-cc-pVDZ and G3MP2 levels. > >However, for the vertical ionization energies, there may be a problem with >using G3MP2. Here's the problem. In the vertical ionization energy >calculation I take the energy of the ion at the same geometry as the >optimized neutral, and subtract the energy of the optimized neutral. The >ion is therefore not at an equilibrium geometry. I am wondering if G3MP2 is >a valid method for calculating the energy of an ion that is not at an >equilibrium geometry. The reason is that a frequency calculation is a part >of the G3MP2 method. The Gaussian website has this to say about frequency >calculations: ""Vibrational frequencies are computed by determining the >second derivatives of the energy with respect to the Cartesian nuclear >coordinates and then transforming to mass-weighted coordinates. This >transformation is only valid at a stationary point! Thus, it is meaningless >to compute frequencies at any geometry other than a stationary point for the >method used for frequency determinatio! > n." This suggests that G3MP2 can't be used to calculate vertical >ionization energies, and in addition, that Gaussian can't be used to >calculate zero point corrections for calculations of vertical ionization >energies. > >Am I correct that G3MP2 can't be used? If so, is there some kind of a fix? >I'd appreciate your input. > >Samuel A. Abrash >Department of Chemistry >University of Richmond >Richmond, VA 23173 >Phone: 804-289-8248 >Fax: 804-287-1897 >E-mail: sabrash**richmond.edu >Web-page: http://oncampus.richmond.edu/~sabrash > >"Rabbi Yitzhak said: At the time God created the world and desired to >reveal the depth of His being from out of the hidden, the light came from >the darkness and they were joined together. Because of this, out of >darkness came the light and out of the hidden came the revealed and out of >the good came evil and out of mercy came severe judgement, and everything is >intertwined with everything else...the good inclination and the evil >inclination, the right and the left." - The Zohar > >-----Original Message----- > > >>From: owner-chemistry**ccl.net [mailto:owner-chemistry**ccl.net] >> >> >Sent: Monday, July 09, 2007 8:24 AM >To: Abrash, Samuel >Subject: CCL:G: Nuclear repulsion energy > > >Sent to CCL by: makowskm(0)chemia.uj.edu.pl > >Is your molecule treated as belonging to C1 symmetry group? If not, the >possible reason is symmetrization that Gaussian does. Means the atoms can >be slightly moved to fit the symmetry group found and as the effect the >standard orientation geometry used in actual calculations can >non-trivially differ from input one. On opposite Gamess has no symmetry >finder and will keep your geometry only translating to center of mass and >rotating to the main axes of inertia tensor. I dont know a bit about ORCA >in this respect. > >Regards, >Marcinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chem >istry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > >