RE: Where to find Mulliken J. Chim. Phys. v.46 p.497 = (1949)?

From owner-chemistry@ccl.net Fri Dec 19 04:23:01 2008 From: "Josep Cester Bofarull josep.cester#urv.cat" To: CCL Subject: CCL: SMILES to VRML or X3D Message-Id: <-38344-081219040500-22292-f4LV2Dbs3gGyu38QZflnmg_._server.ccl.net> X-Original-From: Josep Cester Bofarull Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 19 Dec 2008 09:26:29 +0100 MIME-Version: 1.0 Sent to CCL by: Josep Cester Bofarull [josep.cester : urv.cat] Thank you for your response Rajarshi, as I did with JOELib2, I've succeeded in build a CML file from an SMILES with CDK with this simple code: #### SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IMolecule m = sp.parseSmiles("C(=O)(N)N"); StringWriter output = new StringWriter ( ) ; CMLWriter cmlwriter = new CMLWriter ( output ) ; try { cmlwriter.write ( m ) ; cmlwriter.close ( ) ; } catch ( Exception e ) { System.out.println ( e ) ; } System.out.println("CML: " + output.toString ( ) ); #### The problem I have is that I don't know how to specify 3d coordinates in this CML. Could you give me some example of how to do this? Thank you. Josep En/na Rajarshi Guha ha escrit: > > On Dec 18, 2008, at 8:58 AM, Josep Cester josep.cester]![urv.cat wrote: > >> >> Sent to CCL by: "Josep Cester" [josep.cester===urv.cat] >> Hello, >> >> I need to convert SMILES to VRML or X3D in a java application. Does >> exists any java library to do it? >> >> The only way I've found to get an X3D file from an SMILES is >> converting SMILES to CML (with OpenBabel) and then apply an XSL >> stylesheet to convert CML to X3D. The problem I have is that >> OpenBabel is not written in java. I have also tried JOELib2 to >> convert SMILES to CML, but the CML I get has not got 3D coordinates. > > You can use the CDK to go from SMILES to CML > > ------------------------------------------------------------------- > Rajarshi Guha > GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 > ------------------------------------------------------------------- > "I'd love to go out with you, but my favorite commercial is on TV." > > > -- Josep Cester Bofarull FeT - DEQ Universitat Rovira i Virgili From owner-chemistry@ccl.net Fri Dec 19 08:09:00 2008 From: "Chunhui Li baotogo2004(0)gmail.com" To: CCL Subject: CCL: LogP calculation Message-Id: <-38345-081219080610-4257-mdSF9abtDXjKO2AwyqcpEQ__server.ccl.net> X-Original-From: "Chunhui Li" Date: Fri, 19 Dec 2008 08:06:04 -0500 Sent to CCL by: "Chunhui Li" [baotogo2004###gmail.com] Hi, Everyone! I need to calculate LogP for some molecules and found that there are so many software I can use, such as EPIWIN, ACD, SPARTAN, CLOGP, XLOGP etc. I wonder if there are any review-type paper or other sources which summarize and compare the performance of these different models. I want to know if there is any kind of "gold standard" software to use or which software is suited for which type of molecules. Thanks in advance! Lily From owner-chemistry@ccl.net Fri Dec 19 08:46:00 2008 From: "Seth Olsen s.olsen1=-=uq.edu.au" To: CCL Subject: CCL: Where to find Mulliken J. Chim. Phys. v.46 p.497 (1949)? Message-Id: <-38346-081218230227-13832-x+6Rmy6ORdbaFLdSqYo6OQ^server.ccl.net> X-Original-From: Seth Olsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 19 Dec 2008 13:33:26 +1000 MIME-Version: 1.0 Sent to CCL by: Seth Olsen [s.olsen1*o*uq.edu.au] Hey CCLers, I'm getting frustrated trying to figure out where to get my hands on an apparently famous (or often cited) work by R.S. Mulliken. The citation reads 'J. Chim. Phys. 46 497 (1949)'. I cannot find any citation that does not abbreviate the journal name this way, but I am pretty confident that it stands for Journal de Chimie Physique et de Physico-Chimie Biologique and that the journal no longer exists. Apparently it was subsumed by ChemPhysChem in 1999, but I cannot manage to access the 1949 article from the ChemPhysChem site. My local library doesn't have hard copies of this journal going that far back either... Any ideas? Many Thanks, Seth From owner-chemistry@ccl.net Fri Dec 19 09:24:01 2008 From: "Grace Patlewicz grace.y.tier#,#usa.dupont.com" To: CCL Subject: CCL: LogP calculation Message-Id: <-38347-081219090530-8039-XnSYJcQhdTur4Edm2XfsNw^-^server.ccl.net> X-Original-From: "Grace Patlewicz" Date: Fri, 19 Dec 2008 09:05:26 -0500 Sent to CCL by: "Grace Patlewicz" [grace.y.tier],[usa.dupont.com] A review of available calculators for a range of physchem properties was carried out as part of the guidance preparation for REACH. The report written by John Dearden, Liverpool John Moores University, UK (Dearden J & Worth A (2007). In Silico Prediction of Physicochemical Properties. EUR 23051 EN.) and can be downloaded from the former European Chemicals Bureau website (see http://ecb.jrc.ec.europa.eu/qsar/publications/). This might be a useful starting point. Kind regards Grace Patlewicz From owner-chemistry@ccl.net Fri Dec 19 09:55:00 2008 From: "Wolf-D. Ihlenfeldt wdi#,#xemistry.com" To: CCL Subject: CCL: LogP calculation Message-Id: <-38348-081219094156-20298-pCM3kiOP07ZRWnqrsCr+yQ:server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: en-us Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 19 Dec 2008 15:40:47 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi-$-xemistry.com] See the paper (in press in November) in J. Pharm Sci. by Mannhold, Poda, Ostermann and Tetko.=20 It addresses exactly your question using a 96K cpds dataset (I heard a lecture about this, I do not know if it is already out - maybe you can contact the authors directly) W. D. Ihlenfeldt Xemistry GmbH wdi:+:xemistry.com --- xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt Address: Auf den Stieden 8, D-35094 Lahntal, Germany HR Marburg B4713 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > -----Original Message----- > From: owner-chemistry+wdi=3D=3Dxemistry.com:+:ccl.net [mailto:owner- > chemistry+wdi=3D=3Dxemistry.com:+:ccl.net] On Behalf Of Chunhui Li > baotogo2004(0)gmail.com > Sent: Friday, December 19, 2008 2:06 PM > To: Ihlenfeldt, Wolf D > Subject: CCL: LogP calculation >=20 >=20 > Sent to CCL by: "Chunhui Li" [baotogo2004###gmail.com] > Hi, Everyone! >=20 > I need to calculate LogP for some molecules and found that there are = so > many software I can use, such as EPIWIN, ACD, SPARTAN, CLOGP, XLOGP > etc. I wonder if there are any review-type paper or other sources = which > summarize and compare the performance of these different models. I = want > to know if there is any kind of "gold standard" software to use or > which software is suited for which type of molecules. >=20 > Thanks in advance! >=20 > Lily >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please > change>=20>=20>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search) >=20>=20 From owner-chemistry@ccl.net Fri Dec 19 11:03:00 2008 From: "Ghislain Deslongchamps ghislain=unb.ca" To: CCL Subject: CCL:G: Z-matrix for G03/ONIOM Message-Id: <-38349-081219105939-6154-IT5yU+aQlyxYptlx98PlNA(_)server.ccl.net> X-Original-From: "Ghislain Deslongchamps" Date: Fri, 19 Dec 2008 10:59:35 -0500 Sent to CCL by: "Ghislain Deslongchamps" [ghislain././.unb.ca] Hi all, We are automating some ONIOM calculations in Gaussian03 using SVL/MOE. We noted that the first 3 lines of any z-matrix seem to be hard-coded with the 'H' label, thus forcing those first 3 atoms to be treated at the high computational level in ONIOM. Is there a way to override this, i.e. having a z-matrix where the first 3 atoms are tagged either 'M' or 'L' without having to re-order the z-matrix? Seasons Greetings! Ghislain Deslongchamps From owner-chemistry@ccl.net Fri Dec 19 11:37:00 2008 From: "Giuseppina Gini gini###elet.polimi.it" To: CCL Subject: CCL: LogP calculation Message-Id: <-38350-081219104426-32751-lh9FDXCUFRGoU9H75lzgPA===server.ccl.net> X-Original-From: "Giuseppina Gini" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=utf-8;format="flowed" Date: Fri, 19 Dec 2008 15:53:51 +0100 MIME-Version: 1.0 Sent to CCL by: "Giuseppina Gini" [gini^_^elet.polimi.it] some time ago we made a comparison of different logP for pesticides E. Benfenati, G. Gini, N. Piclin, A. Roncaglioni, M.R. Vari', "Predicting logP of pesticides using different software", Chemosphere , 53, p 1155-1164, 2003. On Fri, 19 Dec 2008 08:06:04 -0500 "Chunhui Li baotogo2004(0)gmail.com" wrote: > > Sent to CCL by: "Chunhui Li" [baotogo2004###gmail.com] > Hi, Everyone! > > I need to calculate LogP for some molecules and found >that there are so many software I can use, such as >EPIWIN, ACD, SPARTAN, CLOGP, XLOGP etc. I wonder if there >are any review-type paper or other sources which >summarize and compare the performance of these different >models. I want to know if there is any kind of "gold >standard" software to use or which software is suited for >which type of molecules. > > Thanks in advance! > > Lily > > > > -= This is automatically added to each message by the >mailing script =- > To recover the email address of the author of the >message, please change > the strange characters on the top line to the {:} sign. >You can also> > E-mail to administrators: CHEMISTRY-REQUEST{:}ccl.net or >use> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, >Password: search)> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > From owner-chemistry@ccl.net Fri Dec 19 12:13:00 2008 From: "Vincent Le Guilloux vincent.le-guilloux!=!univ-orleans.fr" To: CCL Subject: CCL: LogP calculation Message-Id: <-38351-081219101529-13721-8lFBuDSsL5phZ9i0bSdiDw+/-server.ccl.net> X-Original-From: Vincent Le Guilloux Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 19 Dec 2008 15:23:10 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Le Guilloux [vincent.le-guilloux[A]univ-orleans.fr] You should have a look at this recent review on log p calculation: http://www.ncbi.nlm.nih.gov/pubmed/18683876?ordinalpos=3D4&itool=3DEntrezSys= tem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVD= ocSum R. Manhold & al, Calculation of Molecular Lipophilicity: State-of-the-Art an= d Comparison of Log P Methods on More Than 96,000 Compounds, Journal of Phar= maceutical Sciences, 2008 Best regards Bincent Quoting "Chunhui Li baotogo2004(0)gmail.com" : > > Sent to CCL by: "Chunhui Li" [baotogo2004###gmail.com] > Hi, Everyone! > > I need to calculate LogP for some molecules and found that there are so ma= ny software I can use, such as EPIWIN, ACD, SPARTAN, CLOGP, XLOGP etc. I won= der if there are any review-type paper or other sources which summarize and = compare the performance of these different models. I want to know if there i= s any kind of "gold standard" software to use or which software is suited fo= r which type of molecules. > > Thanks in advance! > > Lily > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > > --=20 Vincent Le Guilloux Phd Student - ICOA - UMR CNRS 6005 Div. of chemoinformatic and molecular modeling. University of Orl=E9ans Phone: ++33 2 38 49 45 77 Fax : ++33 2 38 41 72 81 From owner-chemistry@ccl.net Fri Dec 19 13:21:01 2008 From: "Karen.Green-#-sanofi-aventis.com" To: CCL Subject: CCL: Where to find Mulliken J. Chim. Phys. v.46 p.497 (1949)? Message-Id: <-38352-081219131410-26657-bHKOgb5KkySlL43BIev/Cw::server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Type: multipart/related; type="multipart/alternative"; boundary="----_=_NextPart_001_01C96201.05BBD398" Date: Fri, 19 Dec 2008 10:41:28 -0700 MIME-Version: 1.0 Sent to CCL by: [Karen.Green]-[sanofi-aventis.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C96201.05BBD398 Content-Type: multipart/alternative; boundary="----_=_NextPart_002_01C96201.05BBD398" ------_=_NextPart_002_01C96201.05BBD398 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi, Seth, According to Chemical Abstracts SciFinder, the abstract to which you are referring is: ------------------------------------------------------------------------ -------------------------------------------- Bibliographic Information The theory of molecular orbitals. Mulliken, R. S.. Journal de Chimie Physique et de Physico-Chimie Biologique (1949), 46 497-542. CODEN: JCPBAN ISSN: 0021-7689. Journal language unavailable. CAN 44:11690 AN 1950:11690 CAPLUS=20 Abstract The atomic-orbital and mol.-orbital methods are reviewed. The construction of antisymmetrized spin-orbital-product wave functions and the electronic-state wave functions is outlined. Formal expressions are developed for the exact total electronic energy as a sum of the standard configuration energy for state S, the state energy, and the correlation energy. The relatively small magnitude of the correlation energy is illustrated for H and He. The standard-configuration energy for state S is given as (1) the sum of one-electron diagonal energies plus the sum of the Coulomb and exchange integrals, (2) the sum of one-electron self-consistent-field characteristic values minus the Coulomb and exchange integrals, and (3) the sum of the core energy plus one or more one-electron energy terms. By use of (3) for one electron plus core, the Hartree-Slater-Koopmans theorem (that the self-consistent field characteristic value is nearly equal to minus the corresponding vertical ionization energy) is obtained; the accuracy of this theorem is usually aided by partial cancellation of errors as is illustrated for He and H2. The linear-combination-of-atomic-orbitals (LCAO) approximation to the self-consistent-field mol.-orbital method is developed for the case of two-center mol. orbitals occupied by one or two electrons in the field of a core consisting of closed shells. Formulas for computing the atomic integrals and the bond integrals are developed for the homopolar case and from these, the self-consistent field characteristic values for bonding and antibonding. Results of these calcns. indicate that (1) very good practical approximations of all internuclear distances can be obtained from the energy integrals for electronic repulsion; (2) the bond integral is invariant with respect to ionization, the presence of attached atoms, the multiplicity of the bond, and the polarity of the bond, though it varies with internuclear distance and with the type of at. orbital involved; and (3) the at. integral does not show this invariance. There is a crit. analysis of the errors involved in the use of the LCAO approximation in the two-center case. For the heteropolar case, 3 basic parameters are discussed deriving from the at. integrals. These are considered in terms of their counterparts in electronegativity differences. Dipole moments are treated in terms of the LCAO mol.-orbital theory, the total dipole moment assocd. with an electron-pair bond being expressed as the sum of a bond charge moment, an overlap charge moment, a hybridization moment, and a polarization moment. Multiple bonds can be treated in a similar way provided the computed moments of the individual bonds are adjusted to self-consistency. A preliminary calcn. on HCl suggests that the observed moments of the H halides can be explained only if the ps halogen-bonding at. orbital contains a very considerable admixt. of s character.=20 Indexing -- Section 2 (General and Physical Chemistry) =20 Electric moments=20 (calcn. of)=20 Hydrogen halides=20 (elec. moments and mol. orbitals of)=20 Bonds=20 (integrals for homopolar case)=20 Proper functions=20 (orbitals (mol.), theory of)=20 Proper functions=20 (orbitals, theory of) =20 7647-01-0, Hydrochloric acid=20 (elec. moment and mol. orbitals of)=20 1333-74-0, Hydrogen=20 7440-59-7, Helium=20 (orbitals) ------------------------------------------------------------------------ -------------------------------------------- With these ISSN and CODEN numbers a chemistry librarian can help you locate the journal or if you or your advisor is willing, you can order it directly from Chemical Abstracts (see below screenshot): <