From owner-chemistry@ccl.net Fri Apr 4 03:36:00 2008 From: "Andreas Klamt klamt++cosmologic.de" To: CCL Subject: CCL: Early Comp groups in industry Message-Id: <-36641-080404033243-2182-fE7tG0lkSCTbly3TLJjdoA]=[server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 04 Apr 2008 09:32:23 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt%x%cosmologic.de] I just wanted to point to the CASP initiative - Computer Assisted (or maybe Computer Aided) Synthesis Planning - which started in Germany and Switzerland as an initiative of 7 companies in the 1970th, i.e. about ten years before I enter the computational group at Bayer. I know that this laid the foundations for our computational chemistry group at Bayer at that time. All the things which we now consider as trivial as molecular representation, molecular perception, including ring and aromaticity recognition, ... have been developed in that initiative, and we kept working with the molinf library from CASP til the end of the 1990th. But I see that this initative is already mentioned in the book, of Don Boyd. Andreas Boyd, D. boyd[#]chem.iupui.edu schrieb: > Sent to CCL by: "Boyd, D." [boyd!A!chem.iupui.edu] > Allen, > > That would be useful information that you are trying to collect > about the early history. I would be interested in seeing a > summary. > > For a discussion of the early history, I refer you to two book > chapters: > > History of Computers in Pharmaceutical Research and Development: > A Narrative. > D. B. Boyd and M. M. Marsh, in Computer Applications in Pharmaceutical Research > and Development, S. Ekins, Ed., Wiley, > New York, 2006, pp. 1-50. > > How Computational Chemistry Became Important in the Pharmaceutical > Industry. > D. B. Boyd, in Reviews in Computational Chemistry, K. B. Lipkowitz > and T. Cundari, Eds., Wiley-VCH, New York, 2007, Vol. 23, pp. 401- > 451. > > These chapters cite your NetSci website, which is very useful. > > I would send you reprints, but I have none. > > Good luck. > > Don> > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt||cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Apr 4 04:11:00 2008 From: "Andrzej Eilmes eilmes{=}chemia.uj.edu.pl" To: CCL Subject: CCL: CTTC V abstract submission deadline extended Message-Id: <-36642-080404040417-17284-kUjoudttEmk+X+bA2nIG6A===server.ccl.net> X-Original-From: Andrzej Eilmes Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 4 Apr 2008 10:03:59 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Andrzej Eilmes [eilmes(!)chemia.uj.edu.pl] Dear CCL subscribers, As we still receive some late contributions, the deadline for abstract submission for the Conference "Current Trends in Theoretical Chemistry V" (Krakow, Poland, 6-10 July 2008) has been extended to 15 April. All information about the conference (including the list of invited speakers) is available at the conference web page: http://www.chemia.uj.edu.pl/cttc5/ The on-line registration form and the guidelines for abstract preparation are accesible at the same URL. We are looking forward to welcoming you in Krakow in July, Andrzej Eilmes and Jacek Korchowiec -- ------------------------------------------ Current Trends in Theoretical Chemistry V 6-10 July 2008, Krakow, Poland http://www.chemia.uj.edu.pl/cttc5/ From owner-chemistry@ccl.net Fri Apr 4 05:40:02 2008 From: "andras.borosy[A]givaudan.com" To: CCL Subject: CCL: Molecular fragmenter for UNIFAC Message-Id: <-36643-080404045533-17880-K4obge8o3tcACbMWpQQCSw|a|server.ccl.net> X-Original-From: andras.borosy],[givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0030FF3EC1257421_=" Date: Fri, 4 Apr 2008 10:55:10 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy,,givaudan.com This is a multipart message in MIME format. --=_alternative 0030FF3EC1257421_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Collegues, Does an automatic molecular fragmenter for UNIFAC exist? Many thank and best wishes, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com --=_alternative 0030FF3EC1257421_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Collegues,

Does an automatic molecular fragment= er for UNIFAC exist?

Many thank and best wishes,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com --=_alternative 0030FF3EC1257421_=-- From owner-chemistry@ccl.net Fri Apr 4 06:47:00 2008 From: "Marcin Wojdyr wojdyr{=}gmail.com" To: CCL Subject: CCL: ANN: xylib - library for reading x,y data from powder diffraction, XPS Message-Id: <-36644-080404064439-18896-zrTsHeQ04bxeKO0blvjBhQ~!~server.ccl.net> X-Original-From: "Marcin Wojdyr" Date: Fri, 4 Apr 2008 06:44:36 -0400 Sent to CCL by: "Marcin Wojdyr" [wojdyr-#-gmail.com] xylib is a free (LGPL), portable C++ library for reading files that contain x-y data from powder diffraction, spectroscopy or other experimental methods. Supported formats: * plain text * Vamas ISO14976 * Princeton Instruments WinSpec SPE (the formats below are powder diffraction) * CIF for Powder Diffraction (pdCIF) * Siemens/Bruker UXD * Siemens/Bruker RAW v1/2/3 * Philips UDF * Philips RD (raw scan) V3 * Rigaku DAT * Sietronics Sieray CPI * DBWS/DMPLOT data file * Canberra MCA * XFIT/Koalariet XDD * RIET7/LHPM/CSRIET/ILL_D1A5/PSI_DMC DAT Link: http://www.unipress.waw.pl/fityk/xylib/ The library comes with a command-line converting program, and there is also a GUI converting program: http://www.unipress.waw.pl/fityk/xyconvert/ Regards, Marcin From owner-chemistry@ccl.net Fri Apr 4 07:21:01 2008 From: "Wolf-D.Ihlenfeldt wdi!^!xemistry.com" To: CCL Subject: CCL: Molecular fragmenter for UNIFAC Message-Id: <-36645-080404064850-32472-3LXKy+swEPI/4NpqR8+LFQ- -server.ccl.net> X-Original-From: "Wolf-D.Ihlenfeldt" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01C89652.2D8D51A0" Date: Fri, 4 Apr 2008 12:48:25 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D.Ihlenfeldt" [wdi^xemistry.com] Dies ist eine mehrteilige Nachricht im MIME-Format. ------=_NextPart_000_0004_01C89652.2D8D51A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Yes. =20 See www.xemistry.com/fragment=20 =20 For an interactive demo. Commercial in-house licenses and batch = processing tools are also available. =20 =20 =20 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=20 > From: owner-chemistry,ccl.net [mailto:owner-chemistry,ccl.net]=20 Sent: Friday, April 04, 2008 10:55 AM To: Ihlenfeldt, Wolf D Subject: CCL: Molecular fragmenter for UNIFAC =20 Dear Collegues,=20 Does an automatic molecular fragmenter for UNIFAC exist?=20 Many thank and best wishes,=20 Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf = - Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com ------=_NextPart_000_0004_01C89652.2D8D51A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Yes.

 

See www.xemistry.com/fragment

 

For an interactive demo.=A0 Commercial in-house licenses = and batch processing tools are also available.

 

 

 

W. D. Ihlenfeldt
Xemistry GmbH
wdi,xemistry.com
---
xemistry gmbh – 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

From:= owner-chemistry,ccl.net [mailto:owner-chemistry,ccl.net]
Sent: Friday, April 04, 2008 10:55 AM
To: Ihlenfeldt, Wolf D
Subject: CCL: Molecular fragmenter for = UNIFAC

 


Dear = Collegues,

Does = an automatic molecular fragmenter for UNIFAC exist?

Many = thank and best wishes,

Dr. = Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  - =  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http://www.givaudan.com

------=_NextPart_000_0004_01C89652.2D8D51A0-- From owner-chemistry@ccl.net Fri Apr 4 07:57:00 2008 From: "John McKelvey jmmckel,,gmail.com" To: CCL Subject: CCL: Early Comp groups in industry Message-Id: <-36646-080404072210-30901-4C1tl2qZHXndFE4PFtEN+Q.:.server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_9056_27612852.1207307651161" Date: Fri, 4 Apr 2008 07:14:11 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel**gmail.com] ------=_Part_9056_27612852.1207307651161 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Could I add a comment about a "group of 1" at Kodak in the 1960's? There is probably no example of applied MO theory more widely enjoyed by society than the work of David Sturmer at Kodak in Rochester, NY. The problem was that orthochromatic film did not reflect subtle impacts of different colors in black and white photography. This problem was largely eliminated by the use of cyanine dye aggregates on the surface of silver halide crystals. In designing new cyanine dyes David took a simple approach and correlated the computed homo-lumo gap from a specially parameterized Huckel model against the observed Lmax of cyanine dyes. More than reproducing the data used in the fitting procedure, it was very accurately predictive, and was a very handy tool for designing properties of possible dyes. Further, this model was superior to the then existing PPP methods for correlating dye oxidation and reduction potentials. [This was all done without even solving for the eigenvectors of the Huckel matrix, that is solving only the characteristic polynomial.] In the current climate of other approaches that are currently used, such as the latest TDDFT method, I thought people would find this millisecond computational approach amusing, and maybe food [snack?] for thought. Cheers! John McKelvey On Fri, Apr 4, 2008 at 3:32 AM, Andreas Klamt klamt++cosmologic.de < owner-chemistry:+:ccl.net> wrote: > > Sent to CCL by: Andreas Klamt [klamt%x%cosmologic.de] > I just wanted to point to the CASP initiative - Computer Assisted (or > maybe Computer Aided) Synthesis Planning - which started in Germany and > Switzerland as an > initiative of 7 companies in the 1970th, i.e. about ten years before I > enter the computational group at Bayer. I know that this laid the > foundations for our computational chemistry group at Bayer at that time. All > the things which we now consider as trivial as molecular representation, > molecular perception, including ring and aromaticity recognition, ... > have been developed in that initiative, and we kept working with the > molinf library from CASP til the end of the 1990th. > > But I see that this initative is already mentioned in the book, of > Don Boyd. > > Andreas > > > Boyd, D. boyd[#]chem.iupui.edu schrieb: > > > Sent to CCL by: "Boyd, D." [boyd!A!chem.iupui.edu] > > Allen, > > > > That would be useful information that you are trying to collect about > > the early history. I would be interested in seeing a summary. > > > > For a discussion of the early history, I refer you to two book chapters: > > > > History of Computers in Pharmaceutical Research and Development: A > > Narrative. D. B. Boyd and M. M. Marsh, in Computer Applications in > > Pharmaceutical Research > > and Development, S. Ekins, Ed., Wiley, New York, 2006, pp. 1-50. > > > > How Computational Chemistry Became Important in the Pharmaceutical > > Industry. D. B. Boyd, in Reviews in Computational Chemistry, K. B. > > Lipkowitz and T. Cundari, Eds., Wiley-VCH, New York, 2007, Vol. 23, pp. 401- > > 451. > > > > These chapters cite your NetSci website, which is very useful. > > > > I would send you reprints, but I have none. > > > > Good luck. > > > > Don> > > > > > > > > > > > > > -- > > ----------------------------------------------------------------------------- > Dr. habil. Andreas Klamt > COSMOlogic GmbH&CoKG > Burscheider Str. 515 > 51381 Leverkusen, Germany > > Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 > e-mail: klamt^_^cosmologic.de > web: www.cosmologic.de > > ----------------------------------------------------------------------------- > COSMOlogic > Your Competent Partner for > Computational Chemistry and Fluid Thermodynamics > > -----------------------------------------------------------------------------http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_9056_27612852.1207307651161 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Could I add a comment about a "group of 1" at Kodak in the 1960&#= 39;s?  There is probably no example of applied MO theory more widely e= njoyed by society than the work of David Sturmer at Kodak in Rochester, NY.=   The problem was that orthochromatic film did not reflect subtle impa= cts of different colors in black and white photography.  This problem = was largely eliminated by the use of cyanine dye aggregates on the surface = of silver halide crystals.  In designing new cyanine dyes David took a= simple approach and correlated the computed homo-lumo gap from a specially= parameterized Huckel model against the observed Lmax of cyanine dyes. = ; More than reproducing the data used in the fitting procedure, it was very= accurately predictive, and was a very handy tool for designing properties = of possible dyes. Further, this model was superior to the then existing PPP= methods for correlating dye oxidation and reduction potentials. [This was = all done without even solving for the eigenvectors of the Huckel matrix, th= at is solving only the characteristic polynomial.]

In the current  climate of other approaches that are currently use= d, such as  the latest TDDFT method, I thought people would find this = millisecond computational approach amusing, and maybe food [snack?] for tho= ught.

Cheers!

John McKelvey

On Fri, = Apr 4, 2008 at 3:32 AM, Andreas Klamt klamt++cosmologic.de <owner-c= hemistry:+:ccl.net> wrote:

Sent to CCL by: Andreas Klamt [klamt%x%cosmologic.de]
I just wanted to point to the CASP initiative - Computer Assisted (or maybe= Computer Aided) Synthesis Planning - which started in Germany and Switzerl= and as an
initiative of 7 companies in the 1970th, i.e. about ten years before I
enter the computational group at Bayer. I know that this laid the foundatio= ns for our computational chemistry group at Bayer at that time. All the &nb= sp;things which we now consider as trivial as molecular representation, mol= ecular perception, including ring and aromaticity recognition, ...
have been developed in that initiative, and we kept working with the
molinf library from CASP til the end of the 1990th.

But I see that this initative is already mentioned in the book, of
Don Boyd.

Andreas


Boyd, D. boyd[#]chem.iu= pui.edu schrieb:
Sent to CCL by: "Boyd, D." [boyd!A!chem.iupui.edu]
Allen,

That would be useful information that you are trying to collect about the e= arly history.  I would be interested in seeing a summary.

For a discussion of the early history, I refer you to two book chapters:
History of Computers in Pharmaceutical Research and Development: A Narrativ= e. D. B. Boyd and M. M. Marsh, in Computer Applications in Pharmaceutical R= esearch
and Development, S. Ekins, Ed., Wiley, New York, 2006, pp. 1-50.

How Computational Chemistry Became Important in the Pharmaceutical
Industry. D. B. Boyd, in Reviews in Computational Chemistry, K. B. Lipkowit= z and T. Cundari, Eds., Wiley-VCH, New York, 2007, Vol. 23, pp. 401-
451.

These chapters cite your NetSci website, which is very useful.

I would send you reprints, but I have none.

Good luck.

Don>



 


--
---------------------------------------------------------------------------= --
Dr. habil. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: +49-2171-73168-1  Fax:  +49-2171-73168-9
e-mail: klamt^_^cosmolog= ic.de
web:    ww= w.cosmologic.de
---------------------------------------------------------------------------= --
COSMOlogic
     Your Competent Partner for
     Computational Chemistry and Fluid Thermodynamics
---------------------------------------------------------------------------= --



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