From owner-chemistry@ccl.net Thu Aug 23 03:02:01 2007 From: "Tamas Gunda tgunda1%puma.unideb.hu" To: CCL Subject: CCL: Fractional coordinates to cartesian Message-Id: <-34987-070822125715-32194-MmidQXK+hcnisbdZze8wDg%a%server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 22 Aug 2007 17:38:08 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda1,,puma.unideb.hu] Try Mol2Mol. It reads fractional coordinates and can output Cartesian coordinates in a number of different predefined formats or in completly user defined format: http://web.interware.hu/frenzy/mol2mol/ Tamas E. Gunda, D.Sci. Dept. of Pharmaceutical Chemistry University of Debrecen H-4010 Debrecen, POBox 36 Hungary tgunda2 {at} puma.unideb.hu ----- Original Message ----- > From: "Richard Leo Wood woodx278[-]umn.edu" To: "Gunda, Tamas E " Sent: Tuesday, August 21, 2007 15:13 Subject: CCL: Fractional coordinates to cartesian > > Sent to CCL by: "Richard Leo Wood" [woodx278 ~~ umn.edu] > Hi all, > > Do any of you know of any program (free?) that will convert fractional coordinates to cartesian coordinates? If not > in a program, is there a method that can be used to do it? I spent most of yesterday searching for something, but I > came up empty. > > I have a few crystal structures in fractional coordinates (in papers, so I don't have them in electronic format) that > I need converted to cartesian to compare them to some calculations that I have done. > > TIA, > Richard > > > Richard L. Wood, Ph. D. > University of Minnesota > Dept. of Medicinal Chemistry, > College of Pharmacy > 717 Delaware St. SE > Minneapolis, MN 55414-2959 > woodx278[]umn.edu> > > From owner-chemistry@ccl.net Thu Aug 23 03:37:01 2007 From: "Szabolcs Csepregi scsepregi]~[chemaxon.com" To: CCL Subject: CCL: Looking for freeware to compute Tanimoto coefficient Message-Id: <-34988-070823033422-604-nohVwDhwZP6pzDi9gcj3aw-.-server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 23 Aug 2007 08:45:55 +0200 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi^-^chemaxon.com] Hi Manali, You can perform this with the compr utility from the JChem Screen package: http://www.chemaxon.com/jchem/doc/user/Compr.html Alternatively, overlap analysis is available in Instant JChem with similarity option. This will identify the most similar pairs in the two tables depending on your options: http://www.chemaxon.com/anim/ijc/Overlap_analysis.html All ChemAxon products are free under the academic license, and Instant JChem local database mode is free for everyone. I hope this helps. Szabolcs Szabolcs Csepregi, PhD Director of Search Technologies, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 Manali Joshi manali_+_adrik.bchs.uh.edu wrote: > Sent to CCL by: "Manali Joshi" [manali- -adrik.bchs.uh.edu] > Hello, > > I am looking for freeware to compute the Tanimoto coefficients between small molecules. > Specifically i would like to compare a few molecules against a small database. > Thanks in advance. > > -Manali> > > > > From owner-chemistry@ccl.net Thu Aug 23 04:23:01 2007 From: "Lothar Terfloth lothar.terfloth|,|chemie.uni-erlangen.de" To: CCL Subject: CCL: Open Source 3D coordinate generation tool Message-Id: <-34989-070822125824-383-eUiEw27aDNyOdj4fEPZBhw:_:server.ccl.net> X-Original-From: Lothar Terfloth Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 22 Aug 2007 18:00:43 +0200 MIME-Version: 1.0 Sent to CCL by: Lothar Terfloth [lothar.terfloth,chemie.uni-erlangen.de] Dear all, a) SPE is the central step for the generation of a 'rough' set of 3D coordinates in smi23d. Following http://www.wipo.int/pctdb/en/wo.jsp?wo=2004003683&IA=WO2004003683&DISPLAY=STATUS or http://www.wipo.int/pctdb/en/wo.jsp?wo=2004003683&IA=WO2004003683&DISPLAY=STATUS I would assume that there is a patent on the SPE algorithm and its application. Does this affect smi23d? b) Obviously smi2sdf does not support stereochemistry, e.g. butene.smi: C\C=C\C E-but-2-ene C\C=C/C Z-but-2-ene Execution of the following command line smi2sdf -o butene.sdf -p mmff94.prm butene.smi results in identical coordinates for both alkenes. I tried also cis- and trans-decalin. decalin.smi: [H][C++++]12[C++++](CCCC2)([H])CCCC1 cis-decalin [H][C++++]12[C++](CCCC2)([H])CCCC1 trans-decalin Trying to generate the rough 3D coordinates using the following command line smi2sdf -o decalin.sdf -p mmff94.prm decalin.smi results in the following output: Found 2 structures in decalin.smi field : MMFF94 Atom Types: 181 Bonds: 448 Bond3: 0 Bond4: 0 Bond5: 0 Angle: 1801 Angle3: 21 Angle4: 61 Angle5: 0 Torsion: 674 Torsion4: 38 Torsion5: 95 Vdw: 182 OOP: 112 Dipole: 0 Charge: 0 Improper: 0 STBN: 286 ANGANG: 0 STRTOR: 0 VDWPR: 0 Input file = decalin.smi Output file = decalin.sdf Param file = mmff94.prm Log file = error.log Inorganic file = decalin_inorg.smi Structure: 0 [H][C++++]12[C++++](CCCC2)([H])CCCC1 cis-decalin Segmentation fault c) I made a very brief comparision with CORINA on a data set of 146 cytochrome P450 substrates which has been published recently (http://dx.doi.org/10.1021/ci700010t & suppl. material). Hardware: AMD Athlon 64 3200+ 2,2GHz Operating System: openSUSE 10.2 (64bit) >time smi2sdf cyp.smi -o cyp.2d.sdf Found 146 structures in cyp.smi field : MMX Atom Types: 169 Bonds: 580 Bond3: 0 Bond4: 0 Bond5: 0 Angle: 434 Angle3: 41 Angle4: 60 Angle5: 0 Torsion: 697 Torsion4: 58 Torsion5: 0 Vdw: 172 OOP: 91 Dipole: 474 Charge: 0 Improper: 0 STBN: 26 ANGANG: 0 STRTOR: 0 VDWPR: 4 Input file = cyp.smi Output file = cyp.2d.sdf Param file = mmxconst.prm Log file = error.log Inorganic file = cyp_inorg.smi . . . real 0m14.952s user 0m14.925s sys 0m0.020s >time mengine -o cyp.smi2sdf.sdf -p mmff94.prm -c mmxconst.prm cyp.2d.sdf field : MMX Atom Types: 169 Bonds: 580 Bond3: 0 Bond4: 0 Bond5: 0 Angle: 434 Angle3: 41 Angle4: 60 Angle5: 0 Torsion: 697 Torsion4: 58 Torsion5: 0 Vdw: 172 OOP: 91 Dipole: 474 Charge: 0 Improper: 0 STBN: 26 ANGANG: 0 STRTOR: 0 VDWPR: 4 field : MMFF94 Atom Types: 181 Bonds: 448 Bond3: 0 Bond4: 0 Bond5: 0 Angle: 1801 Angle3: 21 Angle4: 61 Angle5: 0 Torsion: 674 Torsion4: 38 Torsion5: 95 Vdw: 182 OOP: 112 Dipole: 0 Charge: 0 Improper: 0 STBN: 286 ANGANG: 0 STRTOR: 0 VDWPR: 0 . . . Ngood: 146 Nbparam: 0 Nbatom: 0 Nbcontact: 0 real 6m10.632s user 5m24.956s sys 0m0.464s >time corina -i t=smiles cyp.smi -o t=sdf cyp.3d.sdf real 0m1.877s user 0m1.824s sys 0m0.036s user time | factor ----------------------------- smi2sdf 0m14.925s | 8 mengine: 5m24.956s | 178 corina: 0m1.824s | 1 For this data set CORINA needs 12.5 ms per compound to generate the 3D coordinates. smi2sdf and mengine need about 2300 ms per compound. In addition to the 3D coordinates mengine calculates some properties (dipole moment, point group, xlog - version 1?, dH, S, dG, CP...) which affect conversion speed. d) How long did it take to generate Pub3D? e) Is mengine based on Pcmodel version 7? ( http://www.serenasoft.com ) With kind regards, Lothar Terfloth P.S.: CORINA is available from Molecular Networks. -------------------------------------------------------- Dr. Lothar Terfloth Tel. +49-9131-9790623 Molecular Networks GmbH Fax: +49-9131-815 669 Henkestr. 91 D-91052 Erlangen Germany email: Lothar.Terfloth++mol-net.com www: http://www.mol-net.com -------------------------------------------------------- From owner-chemistry@ccl.net Thu Aug 23 06:25:00 2007 From: "Rzepa, Henry h.rzepa!A!imperial.ac.uk" To: CCL Subject: CCL: GIAO Magnetic shielding tensor for C-Br systems: an anomaly? Message-Id: <-34990-070823061643-14541-POE+HMywT4oVjPdm1VBwFw[*]server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Thu, 23 Aug 2007 11:15:21 +0100 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa(_)imperial.ac.uk] The isotropic GIAO Magnetic shielding tensor predictions for "organic" like molecules can be remarkably accurate, using eg mpw1pw91/6-31G(d,p), as shown by Rychnovsky for the famous Hexacyclinol saga (with a bit of tweaking, the method gives a mean error for the 23 carbons in this system of 0.9 ppm for the "correct" structure. Contact me for the tweaks!). But attempts to use this method for a related "highly oxygenated" natural product, that happens to have three C-Br bonds, gives an equally good fit for all except the C directly attached to the Br. These are out by 12-15 ppm (all too high). The effect is not basis set dependent (ie 6-311(3d,f), aug-cc-pvdz) and quite a mystery to us. Can anyone on the list offer us an explanation of why the spin 3 79Br nucleus would induce an error in the calculated adjacent C of such magnitude? If the effect is well known, can the error be easily corrected? -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs*|*mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Thu Aug 23 07:35:01 2007 From: "Abraham George abraham.mankavil||gmail.com" To: CCL Subject: CCL: research Message-Id: <-34991-070822140207-21856-qfUGCOLI1iHSLV2QOPitVw^server.ccl.net> X-Original-From: "Abraham George" Content-Type: multipart/alternative; boundary="----=_Part_103838_19310037.1187801767579" Date: Wed, 22 Aug 2007 22:26:07 +0530 MIME-Version: 1.0 Sent to CCL by: "Abraham George" [abraham.mankavil*o*gmail.com] ------=_Part_103838_19310037.1187801767579 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Friend, I am interested. I have a few problems to work on. We will discuss it. Regards, Abraham George (abraham.mankavil^_^gmail.com) On 8/22/07, H H abdallah hwchems=-=yahoo.com wrote: > > > Sent to CCL by: "H H abdallah" [hwchems(a)yahoo.com] > Hello, > I am researcher in the field of theoretical chemistry (QM, MM, MD > simulation ...). Is there any scientist in any field who would like to do > research in this field? I have all the important software for that research > and I want to be the end of this work a publication. > Regards> > > > -- Dr.Abraham George, Reader and Head, Department of Chemistry, Mar Ivanios College, Trivandrum-15. Kerala State. India. 695015. ------=_Part_103838_19310037.1187801767579 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Friend,
                 I am interested.  I have a few problems to work on. We will discuss it.
Regards,
            Abraham George (abraham.mankavil^_^gmail.com)

On 8/22/07, H H abdallah hwchems=-= yahoo.com <owner-chemistry^_^ccl.net> wrote:

Sent to CCL by: "H H abdallah" [hwchems(a)yahoo.com]
Hello,
I am researcher in the field of theoretical chemistry (QM, MM, MD simulation  ...). Is there any scientist in any field who would like to do research in this field? I have all the important software for that research and I want to be the end of this work a publication.
Regards



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--
Dr.Abraham George, Reader and Head, Department of Chemistry,
Mar Ivanios College, Trivandrum-15.
Kerala State. India.
695015. ------=_Part_103838_19310037.1187801767579-- From owner-chemistry@ccl.net Thu Aug 23 08:09:00 2007 From: "Alessandro Contini (alessandro.contini) alessandro.contini]^[unimi.it" To: CCL Subject: CCL: GIAO Magnetic shielding tensor for C-Br systems: an anomaly? Message-Id: <-34992-070823071353-17537-DMaBY7VuaJZ0VAMhiq/Tog[#]server.ccl.net> X-Original-From: "Alessandro Contini (alessandro.contini)" Content-language: it Content-type: multipart/alternative; boundary=--3a1d05e91724f2de92c12 Date: Thu, 23 Aug 2007 13:13:32 +0200 MIME-version: 1.0 Sent to CCL by: "Alessandro Contini (alessandro.contini)" [alessandro.contini-#-unimi.it] This is a multi-part message in MIME format. ----3a1d05e91724f2de92c12 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi=2C what you nare experiencing is the known spin-orbit effect caused b= y heavy atoms like bromine or iodine=2E In the past several methods were= proposed to correct this error=2C take a look at = J=2E Org=2E Chem 2006 Jan 6=3B71(1)=3A159-66 Regards=2C Alessandro ----- Messaggio Originale ----- Da=3A =22Rzepa=2C Henry h=2Erzepa!A!imperial=2Eac=2Euk=22 =3Cowner-chemi= stry=40ccl=2Enet=3E Data=3A Giovedi=27=2C Agosto 23=2C 2007 12=3A32 Oggetto=3A CCL=3A GIAO Magnetic shielding tensor for C-Br systems=3A an = anomaly=3F A=3A =22Contini=2C Alessandro -id=234pv-=22 =3Calessandro=2Econtini=40un= imi=2Eit=3E =3E = =3E Sent to CCL by=3A =22Rzepa=2C Henry=22 =5Bh=2Erzepa(=5F)imperial=2Ea= c=2Euk=5D =3E The isotropic GIAO Magnetic shielding tensor predictions for = =3E =22organic=22 like molecules =3E can be remarkably accurate=2C using eg mpw1pw91/6-31G(d=2Cp)=2C =3E as shown by=A0 Rychnovsky=A0 for the famous=A0 = =3E Hexacyclinol saga =3E (with a bit of tweaking=2C the method gives a mean error for the = =3E 23 carbons in this system of=A0=A0 0=2E9 ppm for the =3E =22correct=22 structure=2E=A0 Contact me for the tweaks!)=2E =3E = =3E But attempts to use this method for a related=A0 =22highly = =3E oxygenated=22natural product=2C that happens to have three=A0 C- =3E Br bonds=2C gives an equally =3E good fit for all except the=A0 C directly attached to the = =3E Br=2E=A0 These are out =3E by=A0 12-15 ppm (all too high)=2E=A0=A0 The effect is not = =3E basis set dependent =3E (ie 6-311(3d=2Cf)=2C=A0 aug-cc-pvdz) and quite a mystery to us=2E =3E = =3E Can anyone on the list offer us an explanation of why the = =3E spin=A0 3 79Br =3E nucleus would induce an error in the=A0 calculated=A0 = =3E adjacent=A0 C of =3E such magnitude=3F=A0 If the effect is well known=2C can the error = =3E be easily =3E corrected=3F = =3E -- = =3E = =3E Henry Rzepa=2E = =3E +44 (020) 7594 5774 (Voice)=3B +44 (0870) 132 3747 (eFax)=3B = =3E rzepahs=5Ba=5Dmac=2Ecom (iChat) =3E =A0http=3A//www=2Ech=2Eic=2Eac=2Euk/rzepa/ Dept=2E Chemistry=2C Impe= rial = =3E College London=2C SW7=A0 2AZ=2C UK=2E = =3E = =3E (Voracious anti-spam filter in operation for received email=2E =3E If expected reply not received=2C please phone/fax)=2E =3E = =3E = =3E = =3E -=3D This is automatically added to each message by the mailing = =3E script =3D- =3E To recover the email address of the author of the message=2C = =3E please change =3E the strange characters on the top line to the =40 sign=2E You can al= so =3E look up the X-Original-From=3A line in the mail header=2E =3E = =3E E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A =3E =A0=A0=A0=A0=A0 http=3A//www=2Eccl=2Enet/cgi- =3E bin/ccl/send=5Fccl=5Fmessage =3E E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use =3E =A0=A0=A0=A0=A0 http=3A//www=2Eccl=2Enet/cgi- =3E bin/ccl/send=5Fccl=5Fmessage =3E Subscribe/Unsubscribe=3A = =3E =A0=A0=A0=A0=A0 = =3E http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml =3E Before posting=2C check wait time at=3A http=3A//www=2Eccl=2Enet =3E = =3E Job=3A http=3A//www=2Eccl=2Enet/jobs = =3E Conferences=3A = =3E http=3A//server=2Eccl=2Enet/chemistry/announcements/conferences/ =3E Search Messages=3A http=3A//www=2Eccl=2Enet/htdig=A0 (login=3A ccl=2C= = =3E Password=3A search) =3E = =3E If your mail bounces from CCL with 5=2E7=2E1 error=2C check=3A =3E =A0=A0=A0=A0=A0 http=3A//www=2Eccl=2Enet/spammers=2Etxt =3E = =3E RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/ =3E = =3E -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- =3E +-+-+-+ =3E = =3E = =3E = =3E = Dr=2E Alessandro Contini Istituto di Chimica Organica =22Alessandro Marchesini=22 Universit=E0=A0 degli Studi di Milano=2C Facolt=E0=A0 di Farmacia Via Venezian=2C 21 20133 Milano = Tel=2E +390250314480 Fax=2E +390250314476 e-mail alessandro=2Econtini=40unimi=2Eit ----3a1d05e91724f2de92c12 Content-Type: text/html; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi=2C what you nare experiencing is the known spin-orbit effect caused b= y heavy atoms like bromine or iodine=2E In the past several methods were= proposed to correct this error=2C take a look at =3Cspan class=3D=22ti=22= =3E=3Cb=3E =3C/b=3E=3Cspan title=3D=22The Journal of organic chemistry=2E= =22=3E=3Cbr=3E=3Cspan style=3D=22text-decoration=3A underline=3B=22=3E=3C= /span=3E=3C/span=3EJ=2E Org=2E Chem 2006 Jan 6=3B71(1)=3A159-66=3Cbr=3E=3C= br=3ERegards=2C=3Cbr=3E=3Cbr=3EAlessandro=3Cbr=3E=3Cbr=3E=3C/span=3E=3Cb= r=3E----- Messaggio Originale -----=3Cbr=3EDa=3A =22Rzepa=2C Henry h=2Er= zepa!A!imperial=2Eac=2Euk=22 =26lt=3Bowner-chemistry=40ccl=2Enet=26gt=3B= =3Cbr=3EData=3A Giovedi=27=2C Agosto 23=2C 2007 12=3A32=3Cbr=3EOggetto=3A= CCL=3A GIAO Magnetic shielding tensor for C-Br systems=3A an anomaly=3F= =3Cbr=3EA=3A =22Contini=2C Alessandro -id=234pv-=22 =26lt=3Balessandro=2E= contini=40unimi=2Eit=26gt=3B=3Cbr=3E=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B Se= nt to CCL by=3A =22Rzepa=2C Henry=22 =5Bh=2Erzepa(=5F)imperial=2Eac=2Euk= =5D=3Cbr=3E=26gt=3B The isotropic GIAO Magnetic shielding tensor predict= ions for =3Cbr=3E=26gt=3B =22organic=22 like molecules=3Cbr=3E=26gt=3B c= an be remarkably accurate=2C using eg mpw1pw91/6-31G(d=2Cp)=2C=3Cbr=3E=26= gt=3B as shown by=26nbsp=3B Rychnovsky=26nbsp=3B for the famous=26nbsp=3B= =3Cbr=3E=26gt=3B Hexacyclinol saga=3Cbr=3E=26gt=3B (with a bit of tweak= ing=2C the method gives a mean error for the =3Cbr=3E=26gt=3B 23 carbons= in this system of=26nbsp=3B=26nbsp=3B 0=2E9 ppm for the=3Cbr=3E=26gt=3B= =22correct=22 structure=2E=26nbsp=3B Contact me for the tweaks!)=2E=3Cb= r=3E=26gt=3B =3Cbr=3E=26gt=3B But attempts to use this method for a rela= ted=26nbsp=3B =22highly =3Cbr=3E=26gt=3B oxygenated=22natural product=2C= that happens to have three=26nbsp=3B C-=3Cbr=3E=26gt=3B Br bonds=2C giv= es an equally=3Cbr=3E=26gt=3B good fit for all except the=26nbsp=3B C di= rectly attached to the =3Cbr=3E=26gt=3B Br=2E=26nbsp=3B These are out=3C= br=3E=26gt=3B by=26nbsp=3B 12-15 ppm (all too high)=2E=26nbsp=3B=26nbsp=3B= The effect is not =3Cbr=3E=26gt=3B basis set dependent=3Cbr=3E=26gt=3B = (ie 6-311(3d=2Cf)=2C=26nbsp=3B aug-cc-pvdz) and quite a mystery to us=2E= =3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B Can anyone on the list offer us an exp= lanation of why the =3Cbr=3E=26gt=3B spin=26nbsp=3B 3 79Br=3Cbr=3E=26gt=3B= nucleus would induce an error in the=26nbsp=3B calculated=26nbsp=3B =3C= br=3E=26gt=3B adjacent=26nbsp=3B C of=3Cbr=3E=26gt=3B such magnitude=3F=26= nbsp=3B If the effect is well known=2C can the error =3Cbr=3E=26gt=3B be= easily=3Cbr=3E=26gt=3B corrected=3F =3Cbr=3E=26gt=3B -- =3Cbr=3E=26gt=3B= =3Cbr=3E=26gt=3B Henry Rzepa=2E =3Cbr=3E=26gt=3B +44 (020) 7594 5774 (V= oice)=3B +44 (0870) 132 3747 (eFax)=3B =3Cbr=3E=26gt=3B rzepahs=5Ba=5Dma= c=2Ecom (iChat)=3Cbr=3E=26gt=3B =26nbsp=3Bhttp=3A//www=2Ech=2Eic=2Eac=2E= uk/rzepa/ Dept=2E Chemistry=2C Imperial =3Cbr=3E=26gt=3B College London=2C= SW7=26nbsp=3B 2AZ=2C UK=2E =3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B (Voracious= anti-spam filter in operation for received email=2E=3Cbr=3E=26gt=3B If = expected reply not received=2C please phone/fax)=2E=3Cbr=3E=26gt=3B =3Cb= r=3E=26gt=3B =3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B -=3D This is automaticall= y added to each message by the mailing =3Cbr=3E=26gt=3B script =3D-=3Cbr= =3E=26gt=3B To recover the email address of the author of the message=2C= =3Cbr=3E=26gt=3B please change=3Cbr=3E=26gt=3B the strange characters o= n the top line to the =40 sign=2E You can also=3Cbr=3E=26gt=3B look up t= he X-Original-From=3A line in the mail header=2E=3Cbr=3E=26gt=3B =3Cbr=3E= =26gt=3B E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A=3Cbr=3E= =26gt=3B =26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B http=3A//www= =2Eccl=2Enet/cgi-=3Cbr=3E=26gt=3B bin/ccl/send=5Fccl=5Fmessage=3Cbr=3E=26= gt=3B E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use=3C= br=3E=26gt=3B =26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B http=3A= //www=2Eccl=2Enet/cgi-=3Cbr=3E=26gt=3B bin/ccl/send=5Fccl=5Fmessage=3Cbr= =3E=26gt=3B Subscribe/Unsubscribe=3A =3Cbr=3E=26gt=3B =26nbsp=3B=26nbsp=3B= =26nbsp=3B=26nbsp=3B=26nbsp=3B =3Cbr=3E=26gt=3B http=3A//www=2Eccl=2Enet= /chemistry/sub=5Funsub=2Eshtml=3Cbr=3E=26gt=3B Before posting=2C check w= ait time at=3A http=3A//www=2Eccl=2Enet=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B= Job=3A http=3A//www=2Eccl=2Enet/jobs =3Cbr=3E=26gt=3B Conferences=3A =3C= br=3E=26gt=3B http=3A//server=2Eccl=2Enet/chemistry/announcements/confer= ences/=3Cbr=3E=26gt=3B Search Messages=3A http=3A//www=2Eccl=2Enet/htdig= =26nbsp=3B (login=3A ccl=2C =3Cbr=3E=26gt=3B Password=3A search)=3Cbr=3E= =26gt=3B =3Cbr=3E=26gt=3B If your mail bounces from CCL with 5=2E7=2E1 e= rror=2C check=3A=3Cbr=3E=26gt=3B =26nbsp=3B=26nbsp=3B=26nbsp=3B=26nbsp=3B= =26nbsp=3B http=3A//www=2Eccl=2Enet/spammers=2Etxt=3Cbr=3E=26gt=3B =3Cbr= =3E=26gt=3B RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instruct= ions/=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-=3Cbr=3E=26gt=3B +-+-+-+=3Cbr=3E=26gt=3B= =3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B =3Cbr=3E=3Cbr=3EDr=2E= Alessandro Contini=3Cbr=3EIstituto di Chimica Organica =22Alessandro Ma= rchesini=22=3Cbr=3EUniversit=E0=26nbsp=3B degli Studi di Milano=2C Facol= t=E0=26nbsp=3B di Farmacia=3Cbr=3EVia Venezian=2C 21 20133 Milano =3Cbr=3E= Tel=2E +390250314480 Fax=2E +390250314476=3Cbr=3Ee-mail alessandro=2Econ= tini=40unimi=2Eit=3Cbr=3E=3Cbr=3E=3Cbr=3E ----3a1d05e91724f2de92c12-- From owner-chemistry@ccl.net Thu Aug 23 08:47:00 2007 From: "Martin Kaupp kaupp##mail.uni-wuerzburg.de" To: CCL Subject: CCL:G: GIAO Magnetic shielding tensor for C-Br systems: an anomaly? Message-Id: <-34993-070823074506-6603-9Tyl6CneRRwjmCU0Pp8z3w%%server.ccl.net> X-Original-From: Martin Kaupp Content-Type: multipart/mixed; boundary="------------050909060106050507090804" Date: Thu, 23 Aug 2007 13:15:36 +0200 MIME-Version: 1.0 Sent to CCL by: Martin Kaupp [kaupp(~)mail.uni-wuerzburg.de] This is a multi-part message in MIME format. --------------050909060106050507090804 Content-Type: multipart/alternative; boundary="------------000208050506080807010705" --------------000208050506080807010705 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Henry, Such heavy-atom effects on the shieldings of certain nuclei ("heavy-atom effect on the light atom shielding") are well-known to arise from spin-orbit contributions (see some references from our own work below). Spin-orbit corrections can be calculated either by relativistic two- or four-component methods (e.g. the ZORA implementation in ADF) or by third-order perturbation theory. The latter methodology is implemented in our MAG-ReSpect code, which can be provided as binary for Linux PCs, and which can read Kohn-Sham MOs from programms like Gaussian. Of the following references, the first book chapter provides the most extensive overview. If you need PDFs, please contact me. Many regards from Wu"rzburg, Martin Reviews: /Relativistic Effects on NMR Chemical Shifts/ M. Kaupp, in /Relativistic Electronic Structure Theory II: Applications/ (Hrsg. P. Schwerdtfeger), series /Theoretical and Computational Chemistry/, Elsevier, Amsterdam 2004. /Interpretation of NMR Chemical Shifts M. Kaupp, in Calculation of NMR and EPR Parameters. Theory and Applications/ (Eds. M. Kaupp, M. Bu"hl, V. G. Malkin) Wiley-VCH, Weinheim 2004. /The DFT Route to NMR Chemical Shifts/ M. Bu"hl, M. Kaupp, V. G. Malkin, O. L. Malkina /J. Comp. Chem./ *1999*, /20/, 91. Some original papers: /How Do Spin-Orbit Induced Heavy-Atom Effects on NMR Chemical Shifts Function? Validation of a Simple Analogy to Spin-Spin Coupling by DFT Calculations on some Iodo Compounds/ M. Kaupp, O. L. Malkina, V. G. Malkin, P. Pyykko" /Chem. Eur. J./ *1998*, /4/, 118. /Study of Relativistic Effects on Nuclear Shieldings Using Density-Functional Theory and Spin-Orbit Pseudopotentials/ J. Vaara, O. L. Malkina, H. Stoll, V. G. Malkin, M. Kaupp /J. Chem. //Phys./ *2001*, 114, 61. /Interpretation of ^13 C NMR Chemical Shifts in Halomethyl Cations. On the Importance of Spin-Orbit Coupling and Electron Correlation/ M. Kaupp, O. L. Malkina, V. G. Malkin /Chem. //Phys. Lett. /*1997*, /265/, 55. /Spin-Orbit Corrections to NMR Shielding Constants from Density Functional Theory. How Important are the Two-Electron Terms?/ O. L. Malkina, B. Schimmelpfennig, M. Kaupp, B. A. Hess, P. Chandra, U. Wahlgren, V. G. Malkin /Chem. Phys. Lett./ *1998*, /296/, 93. /^13 C-NMR Study of Halogen Bonding of Haloarenes. Measurements of Solvent Effects and Theoretical Analysis /R. Glaser, N. Chen, H. Wu, N. Knotts, M. Kaupp/ J. Am. Chem. Soc./ *2004*, /126/, 4412. /Spin-orbit induced anomalous pH dependence in ^1 H NMR spectra of Co^III amine complexes - a diagnostic tool for structure elucidation/ K. Hegetschweiler, D. Kuppert, J. Huppert, M. Straka, M. Kaupp /J. Am. Chem. Soc./ *2004*, /126/, 6728. /The PI_4 ^+ Cation has an Extremely Large Negative ^31 P Chemical Shift, Due to Spin-Orbit Coupling. A Quantum-Chemical Prediction and its Confirmation by Solid-State NMR Spectroscopy/* *M. Kaupp, Ch. Aubauer, G. Engelhardt, T. M. Klapo"tke, O. L. Malkina /J. Chem. //Phys./ *1999*, /110/, 3897. /Characterisation of the Tetrahalophosphonium Cations PBr_n I_4-n ^+ (0 < n < 4) by ^31 P MAS NMR, IR and Raman Spectroscopy and the Crystal Structures of PI_4 ^+ AlCl_4 ^- , PI_4 ^+ AlBr_4 ^- and PI_4 ^+ GaI_4 ^- / C. Aubauer, M. Kaupp, T. M. Klapo"tke, H. No"th, H. Piotrowski, W. Schnick, J. Senker, M. Suter /J. Chem. Soc., Dalton Trans./ *2001*, 1880. /Ab Initio ECP/DFT Analysis of ^13 C and ^1 H Chemical Shifts and Bonding in Mercurimethanes and Organomercury Hydrides: The Role of Scalar Relativistic, Spin-Orbit, and Substituent Effects/ M. Kaupp, O. L. Malkina /J. Chem. Phys./ *1998*, /108/, 3648. MAG-ReSpect, a code for relativistic calculations of NMR and EPR parameters: V. G. Malkin, O. L. Malkina, R. Reviakine, A. V. Arbuznikov, M. Kaupp, B. Schimmelpfennig, I. Malkin, M. Repisky', S. Komorovsky', P. Hrobarik, E. Malkin, T. Helgaker, and K. Ruud, ReSpect, version 2.1, 2006. Rzepa, Henry h.rzepa!A!imperial.ac.uk schrieb: > Sent to CCL by: "Rzepa, Henry" [h.rzepa(_)imperial.ac.uk] > The isotropic GIAO Magnetic shielding tensor predictions for "organic" like molecules > can be remarkably accurate, using eg mpw1pw91/6-31G(d,p), > as shown by Rychnovsky for the famous Hexacyclinol saga > (with a bit of tweaking, the method gives a mean error for the > 23 carbons in this system of 0.9 ppm for the > "correct" structure. Contact me for the tweaks!). > > But attempts to use this method for a related "highly oxygenated" > natural product, that happens to have three C-Br bonds, gives an equally > good fit for all except the C directly attached to the Br. These are out > by 12-15 ppm (all too high). The effect is not basis set dependent > (ie 6-311(3d,f), aug-cc-pvdz) and quite a mystery to us. > > Can anyone on the list offer us an explanation of why the spin 3 79Br > nucleus would induce an error in the calculated adjacent C of > such magnitude? If the effect is well known, can the error be easily > corrected? > --------------000208050506080807010705 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Henry,

Such heavy-atom effects on the shieldings of certain nuclei ("heavy-atom effect on the light atom shielding") are well-known to arise from spin-orbit contributions (see some references from our own work below). Spin-orbit corrections can be calculated either by relativistic two- or four-component methods (e.g. the ZORA implementation in ADF) or by third-order perturbation theory. The latter methodology is implemented in our MAG-ReSpect code, which can be provided as binary for Linux PCs, and which can read Kohn-Sham MOs from programms like Gaussian.

Of the following references, the first book chapter provides the most extensive overview. If you need PDFs, please contact me.
Many regards from Würzburg, Martin

Reviews:
Relativistic Effects on NMR Chemical Shifts M. Kaupp, in Relativistic Electronic Structure Theory II: Applications (Hrsg. P. Schwerdtfeger), series Theoretical and Computational Chemistry, Elsevier, Amsterdam 2004.
Interpretation of NMR Chemical Shifts M. Kaupp, in Calculation of NMR and EPR Parameters. Theory and Applications (Eds. M. Kaupp, M. Bühl, V. G. Malkin) Wiley-VCH, Weinheim 2004.
The DFT Route to NMR Chemical Shifts M. Bühl, M. Kaupp, V. G. Malkin, O. L. Malkina J. Comp. Chem. 1999, 20, 91.

Some original papers:
How Do Spin-Orbit Induced Heavy-Atom Effects on NMR Chemical Shifts Function? Validation of a Simple Analogy to Spin-Spin Coupling by DFT Calculations on some Iodo Compounds M. Kaupp, O. L. Malkina, V. G. Malkin, P. Pyykkö Chem. Eur. J. 1998, 4, 118.
Study of Relativistic Effects on Nuclear Shieldings Using Density-Functional Theory and Spin-Orbit Pseudopotentials J. Vaara, O. L. Malkina, H. Stoll, V. G. Malkin, M. Kaupp J. Chem. Phys. 2001, 114, 61.
Interpretation of 13C NMR Chemical Shifts in Halomethyl Cations. On the Importance of Spin-Orbit Coupling and Electron Correlation M. Kaupp, O. L. Malkina, V. G. Malkin Chem. Phys. Lett. 1997, 265, 55.
Spin-Orbit Corrections to NMR Shielding Constants from Density Functional Theory. How Important are the Two-Electron Terms? O. L. Malkina, B. Schimmelpfennig, M. Kaupp, B. A. Hess, P. Chandra, U. Wahlgren, V. G. Malkin Chem. Phys. Lett. 1998, 296, 93.
13C-NMR Study of Halogen Bonding of Haloarenes.  Measurements of Solvent Effects and Theoretical Analysis R. Glaser, N. Chen, H. Wu, N. Knotts, M. Kaupp J. Am. Chem. Soc. 2004, 126, 4412.
Spin-orbit induced anomalous pH dependence in 1H NMR spectra of CoIII amine complexes - a diagnostic tool for structure elucidation K. Hegetschweiler, D. Kuppert, J. Huppert, M. Straka, M. Kaupp J. Am. Chem. Soc. 2004, 126, 6728.
The PI4+ Cation has an Extremely Large Negative 31P Chemical Shift, Due to Spin-Orbit Coupling. A Quantum-Chemical Prediction and its Confirmation by Solid-State NMR Spectroscopy M. Kaupp, Ch. Aubauer, G. Engelhardt, T. M. Klapötke, O. L. Malkina J. Chem. Phys. 1999, 110, 3897.
Characterisation of the Tetrahalophosphonium Cations PBrnI4-n+ (0 < n < 4) by 31P MAS NMR, IR and Raman Spectroscopy and the Crystal Structures of PI4+AlCl4-, PI4+AlBr4- and PI4+GaI4- C. Aubauer, M. Kaupp, T. M. Klapötke, H. Nöth, H. Piotrowski, W. Schnick, J. Senker, M. Suter J. Chem. Soc., Dalton Trans. 2001, 1880.
Ab Initio ECP/DFT Analysis of 13C and 1H Chemical Shifts and Bonding in Mercurimethanes and Organomercury Hydrides: The Role of Scalar Relativistic, Spin-Orbit, and Substituent Effects M. Kaupp, O. L. Malkina J. Chem. Phys. 1998, 108, 3648.

MAG-ReSpect, a code for relativistic calculations of NMR and EPR parameters: V. G. Malkin, O. L. Malkina, R. Reviakine, A. V. Arbuznikov, M. Kaupp, B. Schimmelpfennig, I. Malkin, M. Repiský, S. Komorovský, P. Hrobarik, E. Malkin, T. Helgaker, and K. Ruud, ReSpect, version 2.1, 2006.




Rzepa, Henry h.rzepa!A!imperial.ac.uk schrieb: 
Sent to CCL by: "Rzepa, Henry" [h.rzepa(_)imperial.ac.uk]
The isotropic GIAO Magnetic shielding tensor predictions for "organic" like molecules
can be remarkably accurate, using eg mpw1pw91/6-31G(d,p),
as shown by  Rychnovsky  for the famous  Hexacyclinol saga
(with a bit of tweaking, the method gives a mean error for the 
23 carbons in this system of   0.9 ppm for the
"correct" structure.  Contact me for the tweaks!).

But attempts to use this method for a related  "highly oxygenated"
natural product, that happens to have three  C-Br bonds, gives an equally
good fit for all except the  C directly attached to the Br.  These are out
by  12-15 ppm (all too high).   The effect is not basis set dependent
(ie 6-311(3d,f),  aug-cc-pvdz) and quite a mystery to us.

Can anyone on the list offer us an explanation of why the spin  3 79Br
nucleus would induce an error in the  calculated  adjacent  C of
such magnitude?  If the effect is well known, can the error be easily
corrected?

--------------000208050506080807010705-- --------------050909060106050507090804 Content-Type: text/plain; name="SIG.txt" Content-Transfer-Encoding: 8bit Content-Disposition: inline; filename="SIG.txt" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Prof. Dr. Martin Kaupp Institut für Anorganische Chemie Universität Würzburg Am Hubland D-97074 Würzburg e-mail:kaupp:_:mail.uni-wuerzburg.de Tel.:0931/888-5281,Fax:0931/888-7135 http://www-anorganik.chemie.uni-wuerzburg.de/kaupp ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --------------050909060106050507090804-- From owner-chemistry@ccl.net Thu Aug 23 09:20:00 2007 From: "chupvl chupvl_-_gmail.com" To: CCL Subject: CCL: Looking for freeware to compute Tanimoto coefficient Message-Id: <-34994-070823060423-13230-+lGU/EsVZYGzPkayKqg/Ow/a\server.ccl.net> X-Original-From: chupvl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 23 Aug 2007 13:07:01 +0400 MIME-Version: 1.0 Sent to CCL by: chupvl [chupvl=-=gmail.com] I think this feature is implemented mostly on chemical cartridges and chemical expert systems. But this cheminf feature is very simple by it's nature - maybe you have to write some kind of script using CDK (or any other descriptors package and) and simple math equitations. I think the Screening Assistant can do this work for you http://www.univ-orleans.fr/icoa/screeningassistant/index.html Vladimir Chupakhin PhD, Dpt. of Chemistry, MSU Moscow , Russia Szabolcs Csepregi scsepregi]~[chemaxon.com wrote: > > Sent to CCL by: Szabolcs Csepregi [scsepregi^-^chemaxon.com] > Hi Manali, > > You can perform this with the compr utility from the JChem Screen > package: > http://www.chemaxon.com/jchem/doc/user/Compr.html > > Alternatively, overlap analysis is available in Instant JChem with > similarity option. This will identify the most similar pairs in the > two tables depending on your options: > http://www.chemaxon.com/anim/ijc/Overlap_analysis.html > > All ChemAxon products are free under the academic license, and Instant > JChem local database mode is free for everyone. > > I hope this helps. > Szabolcs > > Szabolcs Csepregi, PhD > Director of Search Technologies, ChemAxon Ltd. > http://www.chemaxon.com > Skype: szabolcs.csepregi > Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 > > Manali Joshi manali_+_adrik.bchs.uh.edu wrote: >> Sent to CCL by: "Manali Joshi" [manali- -adrik.bchs.uh.edu] >> Hello, >> >> I am looking for freeware to compute the Tanimoto coefficients >> between small molecules. >> Specifically i would like to compare a few molecules against a small >> database. >> Thanks in advance. >> >> -Manalihttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > From owner-chemistry@ccl.net Thu Aug 23 09:55:01 2007 From: "James Asher asher],[mail.uni-wuerzburg.de" To: CCL Subject: CCL:G: ADMP initial velocities Message-Id: <-34995-070822232629-6078-NBZxECVtJgh6eQ7h2GwBpQ(~)server.ccl.net> X-Original-From: James Asher Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Thu, 23 Aug 2007 04:33:54 +0200 MIME-Version: 1.0 Sent to CCL by: James Asher [asher###mail.uni-wuerzburg.de] Hi there, > Sent to CCL by: Konstantin Kudin [konstantin_kudin.:.yahoo.com] > ... When the velocities are set to large values, the nuclei are > suddenly moving fast, but the wavefunctions are still sitting dormant > and have no velocities (at {t-dt} and {t} they were the same). So the > nuclei might be running away from the electrons, before those had a > chance to catch up. I think this is probably the case. If it is, another possible solution would be to make your initial timestep a lot smaller, running a few dozen ADMP steps, and then putting the timestep back to something larger. After a short period with a very small timestep, the electrons and nuclei would be more properly in sync. Hope this helps, James A. > > Regards, > Konstantin > > > > --- "Aviva Litovitz ael23=cornell.edu" wrote: > >> >> Sent to CCL by: "Aviva Litovitz" [ael23-$-cornell.edu] >> I am trying to run ADMP trajectories in gaussian by entering in >> initial velocities (ReadMWVelocity) but it only seems to work if >> these velocities are very small. With larger velocities (~10^13 >> amu1/2*Bohr/sec), after the initial position, the calculation stops >> or the energy balloons and the coordinates turn into asterisks. Any >> suggestions? >> Thanks, >> Aviva > From owner-chemistry@ccl.net Thu Aug 23 10:33:01 2007 From: "Rajarshi Guha rguha|*|indiana.edu" To: CCL Subject: CCL: Looking for freeware to compute Tanimoto coefficient Message-Id: <-34996-070822234303-11788-zLrP9BhtLs7d5nt59tzycA[A]server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 22 Aug 2007 22:38:32 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha,,indiana.edu] On Aug 22, 2007, at 6:04 PM, Manali Joshi manali_+_adrik.bchs.uh.edu wrote: > > Sent to CCL by: "Manali Joshi" [manali- -adrik.bchs.uh.edu] > Hello, > > I am looking for freeware to compute the Tanimoto coefficients > between small molecules. > Specifically i would like to compare a few molecules against a > small database. > Thanks in advance. The CDK (http://almost.cubic.uni-koeln.de/cdk) will do this, but you'd need to write some code (to read n structures and evaluate the similarity) ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Mathematics consists of proving the most obvious thing in the least obvious way. -- George Polya From owner-chemistry@ccl.net Thu Aug 23 11:05:01 2007 From: "Mesa Analytics & Computing, LLC mesaac]*[comcast.net" To: CCL Subject: CCL: Looking for freeware to compute Tanimoto coefficient Message-Id: <-34997-070823092615-12315-TyPh6nct0VSbnkICbo8XTA++server.ccl.net> X-Original-From: "Mesa Analytics & Computing, LLC" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 23 Aug 2007 06:54:21 -0600 MIME-Version: 1.0 Sent to CCL by: "Mesa Analytics & Computing, LLC" [mesaac::comcast.net] Manali, We offer -- free to academics -- a compound fingerprinter and similarity/cluster analysis tools (includes calculating various coefficients such as the Tanimoto). The fingerprinter requires an additional OpenEye Scientific academic license (http://www.eyesopen.com). See www.mesaac.com for more information. Cheers, Norah MacCuish, Ph.D. CSO Mesa Analytics & Computing, LLC Tel: (505)983-3449 www.mesaac.com Manali Joshi manali_+_adrik.bchs.uh.edu wrote: >Sent to CCL by: "Manali Joshi" [manali- -adrik.bchs.uh.edu] >Hello, > >I am looking for freeware to compute the Tanimoto coefficients between small molecules. >Specifically i would like to compare a few molecules against a small database. >Thanks in advance. > >-Manali> > > > > > > From owner-chemistry@ccl.net Thu Aug 23 11:45:01 2007 From: "Igor Filippov Contr igorf(0)helix.nih.gov" To: CCL Subject: CCL: Looking for freeware to compute Tanimoto coefficient Message-Id: <-34998-070823104943-14558-CvfYaKjXDQt5ufTCxTAHLA^-^server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 23 Aug 2007 10:49:28 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf ~~ helix.nih.gov] A simple CACTVS script can do this for you too: ---------------------------- set smiles1 [lindex $argv 0] set smiles2 [lindex $argv 1] #prop setparam E_SCREEN extended 2 # to select extended fingerprint if {![catch {ens create $smiles1} eh1]} { if {![catch {ens create $smiles2} eh2]} { ens hadd $eh1 ens hadd $eh2 set scr1 [ens get $eh1 E_SCREEN] set scr2 [ens get $eh2 E_SCREEN] set l [string length $scr1] set sum1 0 set sum2 0 set sum_both 0 for {set i 0} {$i < $l} {incr i} { set b1 [string index $scr1 $i] set b2 [string index $scr2 $i] set sum1 [expr {$sum1+$b1}] set sum2 [expr {$sum2+$b2}] set bb [expr {$b1 & $b2}] set sum_both [expr {$sum_both+$bb}] } set tanimoto [expr {1.*$sum_both/($sum1+$sum2-$sum_both)}] puts $tanimoto } } exit --------------------------------------- Igor On Thu, 2007-08-23 at 13:07 +0400, chupvl chupvl_-_gmail.com wrote: > Sent to CCL by: chupvl [chupvl=-=gmail.com] > I think this feature is implemented mostly on chemical cartridges and > chemical expert systems. > But this cheminf feature is very simple by it's nature - maybe you have > to write some kind of script using CDK (or any other descriptors package > and) and simple math equitations. > > I think the Screening Assistant can do this work for you > http://www.univ-orleans.fr/icoa/screeningassistant/index.html > > Vladimir Chupakhin > PhD, Dpt. of Chemistry, MSU > Moscow , Russia > > Szabolcs Csepregi scsepregi]~[chemaxon.com wrote: > > > > Sent to CCL by: Szabolcs Csepregi [scsepregi^-^chemaxon.com] > > Hi Manali, > > > > You can perform this with the compr utility from the JChem Screen > > package: > > http://www.chemaxon.com/jchem/doc/user/Compr.html > > > > Alternatively, overlap analysis is available in Instant JChem with > > similarity option. This will identify the most similar pairs in the > > two tables depending on your options: > > http://www.chemaxon.com/anim/ijc/Overlap_analysis.html > > > > All ChemAxon products are free under the academic license, and Instant > > JChem local database mode is free for everyone. > > > > I hope this helps. > > Szabolcs > > > > Szabolcs Csepregi, PhD > > Director of Search Technologies, ChemAxon Ltd. > > http://www.chemaxon.com > > Skype: szabolcs.csepregi > > Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 > > > > Manali Joshi manali_+_adrik.bchs.uh.edu wrote: > >> Sent to CCL by: "Manali Joshi" [manali- -adrik.bchs.uh.edu] > >> Hello, > >> > >> I am looking for freeware to compute the Tanimoto coefficients > >> between small molecules. > >> Specifically i would like to compare a few molecules against a small > >> database. > >> Thanks in advance. > >> > >> -Manalihttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Thu Aug 23 12:14:01 2007 From: "Alexandra Tavares Marques alexandra.marques%fc.up.pt" To: CCL Subject: CCL:G: ONIOM problem Message-Id: <-34999-070823111306-30352-pzofHYUuoUsaVGNkCJ7vLw---server.ccl.net> X-Original-From: "Alexandra Tavares Marques" Date: Thu, 23 Aug 2007 11:13:03 -0400 Sent to CCL by: "Alexandra Tavares Marques" [alexandra.marques]![fc.up.pt] Hi I want to do a PES scan in Gaussian, using the ONIOM method to assign two layers to my protein. Here is a small part of my input: %chk=amber.chk %nproc=1 %mem=65MW p oniom=(B3LYP/SDD:amber(softfirst)) scf(maxcycles=500,xqc,tight) geom(nodistance,noangle) gfinput gfprint test opt(maxcycles=500,modredundant,gdiis) scan -14 1 -4 1 -10 1 N-N3-0.173700 -1 34.635000 46.906000 31.715000 L H-H-0.192100 -1 33.740000 47.296000 31.984000 L H-H-0.192100 -1 35.284000 47.671000 31.589000 L H-H-0.192100 -1 34.960000 46.273000 32.439000 L C-CT-0.073300 -1 34.502000 46.182000 30.441000 L HrmBnd1 HC CC NA 80.0 109.6 B 10451 10821 S 11 -0.50 However the calculation stops in the first optimization. The last lines of the output are: Item Value Threshold Converged? Maximum Force 0.216472 0.000450 NO RMS Force 0.034705 0.000300 NO Maximum Displacement 0.635458 0.001800 NO RMS Displacement 0.104954 0.001200 NO Maximum MM Force 0.028197 0.000045 NO RMS MM Force 0.002357 0.000030 NO Predicted change in Energy=-1.320562D-01 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Fragment: 1 Trans scale: 1.0000 Rot scale: 0.0429 NRF= 1 NRA= 100 NVA=3643 HaveQM=F Convergence limit is 0.300E-04 MaxStp= 33639 StMxLn= 1.00D-04 StpMin= 1.00D-06. Convergence criteria 0.00004500 0.00003000 0.00018000 0.00012000 Step NS ND Rises OKQ Scale Max. Force RMS Force Max. Disp. RMS Disp. Energy Flag 1 0 0 F T 1.00D+00 0.29833317 0.00650682 0.14174897 0.00364059 -38.5041630 ---- 2 0 0 F F -4.34D-01 0.29833317 0.00650682 0.14174897 0.00364059 -38.5358748 ---- 3 0 0 F F -9.78D-04 0.29833317 0.00650682 0.06155179 0.00158085 -38.5842445 ---- .. 574 0 0 T F 3.25D-01********************** 0.01204924 0.00012232 -47.0096788 ---- 575 0 0 T F 3.11D-01********************** 0.00392128 0.00003981 -65.9434982 ---+ 576 0 0 T F 2.78D-01********************** 0.00121932 0.00001238 -135.6763048 ---+ 577 0 0 T F 3.43D-01********************** 0.00033872 0.00000344 -577.9112043 ---+ 578 0 0 F T 1.00D+00********************************************-2978.0923218 ---- I have already added the options scf=xqc and opt=gdiis to the input but the problem continue. Does anyone know what may be causing this problem and how to solve it? I also noted two weird things in the .log file: 1) Warning! P atom10823 may be hypervalent but has no d functions. Warning! P atom10827 may be hypervalent but has no d functions. These two P atoms are in the high layer. What these lines mean? Am I missing to add some option in the input file? 2) Pseudopotential Parameters =================================================================================================================================== Center Atomic Valence Angular Power Coordinates Number Number Electrons Momentum of R Exponent Coefficient X Y Z =================================================================================================================================== 1 7 46.796865 37.753934-18.704245 No pseudopotential on this center. *** 30 20 -1.821746 -5.665497-17.652697 F and up 2 1.0000000 0.00000000 S - F 2 34.1500000 399.98728200 2 14.5900000 85.48565500 P - F 2 39.7800000 277.14896000 2 14.9500000 69.05220500 D - F 2 43.8000000 -34.14934900 2 14.9800000 -3.29183100 This happens for all atoms excepting for a Zn atom. Is this normal? I am new gaussians user. Any help is highly appreciated. Thanks Alexandra From owner-chemistry@ccl.net Thu Aug 23 12:50:00 2007 From: "Efrat Noy enoy%a%epixpharma.com" To: CCL Subject: CCL: fragment-substructure search Message-Id: <-35000-070823112445-8492-symDzLKxK28Vc1o5rFyrgA]*[server.ccl.net> X-Original-From: "Efrat Noy" Date: Thu, 23 Aug 2007 11:24:40 -0400 Sent to CCL by: "Efrat Noy" [enoy++epixpharma.com] Hi All, I am looking for a tool capable of counting non-overlapping instances of substructure-fragments in a set of molecules, yet counting partially overlapping fragments. For example, counting two instances of a benzene fragment in a naphtalene molecule. Are you familiar with any tool able to do that? Thanks enoy=epixpharma.com From owner-chemistry@ccl.net Thu Aug 23 14:03:01 2007 From: "david.giesen_._kodak.com" To: CCL Subject: CCL: GIAO Magnetic shielding tensor for C-Br systems: an anomaly? Message-Id: <-35001-070823094509-28188-npaEEgkIzIjXbLvJfIMzTQ++server.ccl.net> X-Original-From: david.giesen!^!kodak.com Content-Type: text/plain; charset="US-ASCII" Date: Thu, 23 Aug 2007 08:34:22 -0400 MIME-Version: 1.0 Sent to CCL by: david.giesen[A]kodak.com Carbons attached to the halide atoms have significant spin-orbit coupling effects on the NMR shifts that make them outliers compared to other carbon atoms. For an example of how carbons attached to Cl, Br and I atoms can be treated, see: Giesen and Zumbulyadis, Phys Chem Chem Phys, 2002, 4, 5498 A reference for the spin orbit coupling effect on the NMR shifts of C-halide atoms is: Kaupp, Malkina and Malkin, Chem Phys Lett, 1997, 265, 55. Dave Giesen owner-chemistry() ccl.net wrote on 08/23/2007 06:15:21 AM: > > Sent to CCL by: "Rzepa, Henry" [h.rzepa(_)imperial.ac.uk] > The isotropic GIAO Magnetic shielding tensor predictions for > "organic" like molecules > can be remarkably accurate, using eg mpw1pw91/6-31G(d,p), > as shown by Rychnovsky for the famous Hexacyclinol saga > (with a bit of tweaking, the method gives a mean error for the > 23 carbons in this system of 0.9 ppm for the > "correct" structure. Contact me for the tweaks!). > > But attempts to use this method for a related "highly oxygenated" > natural product, that happens to have three C-Br bonds, gives an equally > good fit for all except the C directly attached to the Br. These are out > by 12-15 ppm (all too high). The effect is not basis set dependent > (ie 6-311(3d,f), aug-cc-pvdz) and quite a mystery to us. > > Can anyone on the list offer us an explanation of why the spin 3 79Br > nucleus would induce an error in the calculated adjacent C of > such magnitude? If the effect is well known, can the error be easily > corrected? > > From owner-chemistry@ccl.net Thu Aug 23 14:35:01 2007 From: "Aviva Litovitz ael23|cornell.edu" To: CCL Subject: CCL:G: ADMP initial velocities Message-Id: <-35002-070823142851-31905-vj/eRwjKxq4DW6CL7oabVw ~ server.ccl.net> X-Original-From: "Aviva Litovitz" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 23 Aug 2007 14:28:32 -0400 MIME-Version: 1.0 Sent to CCL by: "Aviva Litovitz" [ael23:-:cornell.edu] Thanks, Konstantin and James! If I understand you correctly, it still doesn't work. I took a geometry and corresponding velocities from several steps into a BOMD calculation and used that as input for ADMP and had the same problem. I have had no problems with BOMD but can't use it as it's prohibitively slow. I've run ADMP calculations _without_ initial velocities and used the geometry and velocities > from several steps in to start another ADMP calculation and had the same problem. But in all of these cases, the wavefunctions start out at static positions, correct? Although, isn't that also the case when ADMP generates its own initial velocities? I've also tried smaller time steps in ADMP (down to 0.0001 fs) without success - although smaller steps did allow larger velocities - just not as large as I need. I guess I could try even smaller steps but it starts being ridiculous. Best, Aviva ----- Original Message ----- > From: "Konstantin Kudin konstantin_kudin~!~yahoo.com" To: "Litovitz, Aviva " Sent: Wednesday, August 22, 2007 7:02 PM Subject: CCL:G: ADMP initial velocities > > Sent to CCL by: Konstantin Kudin [konstantin_kudin.:.yahoo.com] > Hi Aviva, > > Perhaps, the first thing to try is to check if the BOMD could run with > the same input. If that is OK, then your problem could be due to the > following. When the velocities are set to large values, the nuclei are > suddenly moving fast, but the wavefunctions are still sitting dormant > and have no velocities (at {t-dt} and {t} they were the same). So the > nuclei might be running away from the electrons, before those had a > chance to catch up. To fix this one could input velocities, do a few > BOMD steps, and then restart with ADMP such that the wavefunctions at > this point are moving in sync with the nuclei. > > Please post back if this helped. > > Regards, > Konstantin > > > > --- "Aviva Litovitz ael23=cornell.edu" wrote: > >> >> Sent to CCL by: "Aviva Litovitz" [ael23-$-cornell.edu] >> I am trying to run ADMP trajectories in gaussian by entering in >> initial velocities (ReadMWVelocity) but it only seems to work if >> these velocities are very small. With larger velocities (~10^13 >> amu1/2*Bohr/sec), after the initial position, the calculation stops >> or the energy balloons and the coordinates turn into asterisks. Any >> suggestions? >> Thanks, >> Aviva >> >> >> >> -= This is automatically added to each message by the mailing script >> =- >> To recover the email address of the author of the message, please >> change> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >> search)> >> >> >> > > > > > ____________________________________________________________________________________ > Be a better Heartthrob. Get better relationship answers from someone who > knows. Yahoo! Answers - Check it out. > http://answers.yahoo.com/dir/?link=list&sid=396545433> > > From owner-chemistry@ccl.net Thu Aug 23 15:34:00 2007 From: "Joseph Durant jdurant%mdl.com" To: CCL Subject: CCL: fragment-substructure search Message-Id: <-35003-070823152032-3067-FZTTgN0XTxTZiNiJgQRmpg(~)server.ccl.net> X-Original-From: Joseph Durant Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 23 Aug 2007 11:26:33 -0700 MIME-Version: 1.0 Sent to CCL by: Joseph Durant [jdurant-*-mdl.com] Hi Efrat, MDL's Cheshire will allow you to do that; you can use the FILTER_SYMMETRY parameter with MapIterator() to suppress the multiple mappings of, for example, benzene on benzene, but still map benzene twice on napthalene. Then you count the mappings. Joe -- Joe Durant jdurant-,-mdl.com Elsevier MDL 2440 Camino Ramon, Suite 300, San Ramon, CA 94583 voice: (925) 543-7511 -------------- "He has a PhD in theoretical physics. I would be more impressed if it was real physics." Ronnie Cox Efrat Noy enoy%a%epixpharma.com wrote: > Sent to CCL by: "Efrat Noy" [enoy++epixpharma.com] > Hi All, > > I am looking for a tool capable of counting non-overlapping instances of substructure-fragments in a set of molecules, yet counting partially overlapping fragments. For example, counting two instances of a benzene fragment in a naphtalene molecule. > > Are you familiar with any tool able to do that? > > Thanks > > > > > enoy]_[epixpharma.com> > > From owner-chemistry@ccl.net Thu Aug 23 17:08:00 2007 From: "TJ O Donnell tjo(!)acm.org" To: CCL Subject: CCL: fragment-substructure search Message-Id: <-35004-070823165214-19956-WqZzB7pbKs/mARKt/9zl/A(-)server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 23 Aug 2007 13:51:51 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo===acm.org] The gNova cartridge has a count_matches function that will count overlapping and non-overlapping occurrences of substructures, specified as SMARTS. The function can be applied to a single structure, specified as SMILES, or to an entire database of comounds. TJ O'Donnell http://www.gnova.com Efrat Noy enoy%a%epixpharma.com wrote: > Sent to CCL by: "Efrat Noy" [enoy++epixpharma.com] > Hi All, > > I am looking for a tool capable of counting non-overlapping instances of substructure-fragments in a set of molecules, yet counting partially overlapping fragments. For example, counting two instances of a benzene fragment in a naphtalene molecule. > > Are you familiar with any tool able to do that? > > Thanks From owner-chemistry@ccl.net Thu Aug 23 19:42:01 2007 From: "Green Power powergreen%a%gmail.com" To: CCL Subject: CCL: Semi empirical PBC program Message-Id: <-35005-070823180318-17966-YlFieNXJrc2T5kex/YFVSw{}server.ccl.net> X-Original-From: "Green Power" Content-Type: multipart/alternative; boundary="----=_Part_129293_23980306.1187902706743" Date: Thu, 23 Aug 2007 16:58:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Green Power" [powergreen=gmail.com] ------=_Part_129293_23980306.1187902706743 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All, Can you recommed a free semiempirical PBC program, which can perform geometry optimization? Thank you in advance. Tian ------=_Part_129293_23980306.1187902706743 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear All,
 
Can you recommed a free semiempirical PBC program, which can perform geometry optimization? Thank you in advance.
 
Tian 
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