=0A

Mathematica has some new feature ava= ilable in version 7 -

=0A

But how comprehensive it is i don't kno= w!

=0A

From the Mathematic= a help files:

=0A

Chemicals can be specified b= y their common names such as "Water" or "AceticAcid", registry numbers such as "CID96= 2" or "CAS732-18-5", IUPAC-like names such a= s "2Methylpropane" or structure strings.

= =0A

ChemicalData[] gives a list of all= available chemicals.

=0A

ChemicalData["Properties"] gives a list of all properties available for chemic= als.

=0A

So if your compunds are common = enough to be found there, you would type:

=0A

= =0A

ChemicalData["CAS22839-47-0", "SMILES"]

So to automate= it, you would make a list of the CAS numbers, and then apply the func= tion to the list and capture the answer in a new list, which you could then= manipulate however you like.

=0A

= =0A

Let me know if it works - i tend to think of Mathematica's dat= abases as frivolous.

=0A

It might restore my f= aith to see somebody actually use them!

"Most folks are about as= happy as they make up their minds to be." - Abraham Lincoln=

=0A

=0AFrom: Rajarshi Guha rajarshi.guha+*+gmail.com <= ;owner-chemistry_-_ccl.net>
To: "Theel, Kelly " <smilin_iis_-_yahoo.com>
Sent: Thursday, September 10, 2009 10= :29:42 AM
Subject: CCL: = CAS number to Smile String

=0A

On Thu, Sep 10, 2009 at 12:27 PM, Chunhui Li baotogo2004#,#gmail.com <owner-chemistry]=3D= [ccl.net> wrote:
=0A

Sent to CCL by: "Chunhui Li" [baotogo2004_._gmail.com]
H= i Dear ALl,

I want to generate smile strings for more than 100 chemi= cals. All I have is the CAS number for each chemical. Is there any tools I = can use to do this automatically?

=0A

One way to ge= t it is to use the PubChem synonym tables - this is obviously not a compreh= ensive solution as it doesn't contain the entire CAS registry.

There= 's a simple REST interface (based on a mirror of PubChem at IU). For exampl= e, given a CAS for aspirin visit

http://toposome.chemistry.drexel.edu/~rguha/rest/db/pubchem/cas2sm= i/69-46-5

and you get back the SMILES for it. In general, replac= e the CAS at the end of the URL to whatever you want

--
Rajarshi Guha
NIH Chemical Genomics Center

--0-720604125-1252615019=:53735-- From owner-chemistry@ccl.net Thu Sep 10 18:01:01 2009 From: "Wolf-D. Ihlenfeldt wdi::xemistry.com" To: CCL Subject: CCL: CAS number to Smile String Message-Id: <-40214-090910152054-5448-9T+6zVdGjObpWNsfrNtXYg!=!server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_00AB_01CA325C.87812BD0" Date: Thu, 10 Sep 2009 21:20:31 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi=-=xemistry.com] This is a multi-part message in MIME format. ------=_NextPart_000_00AB_01CA325C.87812BD0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 Dear Chunhui, =20 In case you do not want to type in a hundred CAS numbers on a Web = interface, you can use the Cactvs toolkit (free academic versions at www.xemistry.com/academic) and write a tiny script: =20 molfile loop =93myfile.cas=94 eh { echo [ens get $eh E_SMILES] } =20 Internally, this tries both the REST service at http://cactus.nci.nih.gov/cgi-bin/lookup/search (developed by Markus Sitzmann) and PubChem (the up-to-date original, not a mirror, via NCBI eutils) =20 myfile.cas is a text file with CAS numbers, one per line. Bulletproofing = the script for CAS numbers which cannot be resolved etc. is left as an = exercise to the user =96 please consult the extensive documentation of the = toolkit. =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+wdi=3D=3Dxemistry.com-#-ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com-#-ccl.net] On Behalf Of = Rajarshi Guha rajarshi.guha+*+gmail.com Sent: Thursday, September 10, 2009 7:30 PM To: Ihlenfeldt, Wolf D Subject: CCL: CAS number to Smile String =20 =20 On Thu, Sep 10, 2009 at 12:27 PM, Chunhui Li baotogo2004#,#gmail.com wrote: Sent to CCL by: "Chunhui Li" [baotogo2004_._gmail.com] Hi Dear ALl, I want to generate smile strings for more than 100 chemicals. All I have = is the CAS number for each chemical. Is there any tools I can use to do = this automatically? One way to get it is to use the PubChem synonym tables - this is = obviously not a comprehensive solution as it doesn't contain the entire CAS = registry. There's a simple REST interface (based on a mirror of PubChem at IU). = For example, given a CAS for aspirin visit http://toposome.chemistry.drexel.edu/~rguha/rest/db/pubchem/cas2smi/69-46= -5 and you get back the SMILES for it. In general, replace the CAS at the = end of the URL to whatever you want --=20 Rajarshi Guha NIH Chemical Genomics Center ------=_NextPart_000_00AB_01CA325C.87812BD0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Chunhui,

In case you do not want to type in a hundred CAS numbers = on a Web interface, you can use the Cactvs toolkit (free academic versions at = www.xemistry.com/academic) = and write a tiny script:

molfile loop “myfile.cas” eh = {

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 echo [ens = get $eh E_SMILES]

}

Internally, this tries both =A0the REST service at http://cactus.nc= i.nih.gov/cgi-bin/lookup/search (developed by Markus Sitzmann) and PubChem (the up-to-date original, not = a mirror, via NCBI eutils)

myfile.cas is a text file with CAS numbers, one per line. Bulletproofing the script for CAS numbers which cannot be resolved etc. = is left as an exercise to the user – please consult the extensive = documentation of the toolkit.

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+wdi=3D=3Dxemistry.com-#-ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com-#-ccl.net] On Behalf Of = Rajarshi Guha rajarshi.guha+*+gmail.com
Sent: Thursday, September 10, 2009 7:30 PM
To: Ihlenfeldt, Wolf D
Subject: CCL: CAS number to Smile String

On Thu, Sep 10, 2009 at 12:27 PM, Chunhui Li = baotogo2004#,#gmail.com <owner-chemistry]=3Dcl.net&g= t; wrote:

Sent to CCL by: "Chunhui Li" [baotogo2004_._gmail.com]
Hi Dear ALl,

I want to generate smile strings for more than 100 chemicals. All I have = is the CAS number for each chemical. Is there any tools I can use to do this automatically?

One way to get it is to use the PubChem synonym tables - this is = obviously not a comprehensive solution as it doesn't contain the entire CAS = registry.

There's a simple REST interface (based on a mirror of PubChem at IU). = For example, given a CAS for aspirin visit

http://toposome.chemistry.drexel.edu/~rguha/rest/db/pubchem/c= as2smi/69-46-5

and you get back the SMILES for it. In general, replace the CAS at the = end of the URL to whatever you want

--
Rajarshi Guha
NIH Chemical Genomics Center

------=_NextPart_000_00AB_01CA325C.87812BD0-- From owner-chemistry@ccl.net Thu Sep 10 18:35:00 2009 From: "Markus Sitzmann sitzmann---helix.nih.gov" To: CCL Subject: CCL: CAS number to Smile String Message-Id: <-40215-090910141426-23302-kJWn53U4EtQKeaOM5hrX0A]~[server.ccl.net> X-Original-From: Markus Sitzmann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 10 Sep 2009 13:40:32 -0400 MIME-Version: 1.0 Sent to CCL by: Markus Sitzmann [sitzmann**helix.nih.gov] Chunhui, you might try our NCI/CADD Chemical Identifier Resolver at http://cactus.nci.nih.gov/chemical/structure If the service knows the CAS number converting the CAS number to SMILES string is just: http://cactus.nci.nih.gov/chemical/structure/64-17-5/smiles or, converting it to SDF file: http://cactus.nci.nih.gov/chemical/structure/64-17-5/file?format=sdf Markus Chunhui Li baotogo2004#,#gmail.com wrote: > Sent to CCL by: "Chunhui Li" [baotogo2004_._gmail.com] > Hi Dear ALl, > > I want to generate smile strings for more than 100 chemicals. All I have is the CAS number for each chemical. Is there any tools I can use to do this automatically? > > Thanks in advance!> > -- Markus Sitzmann, Ph.D. Laboratory of Medicinal Chemistry Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzmann(!)helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann From owner-chemistry@ccl.net Thu Sep 10 19:35:01 2009 From: "Serguei Patchkovskii ps _ ned.sims.nrc.ca" To: CCL Subject: CCL:G: strange spin annihilation Message-Id: <-40216-090910182338-20306-PQFb5la+pQw498Z44gXhmg_-_server.ccl.net> X-Original-From: Serguei Patchkovskii Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 10 Sep 2009 17:53:38 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Serguei Patchkovskii [ps%ned.sims.nrc.ca] Steve, The calculation you are trying to do is meaningless. So the results you get are also meaningless - and you should not waste your time trying to interpret them in any way. The system you are looking at is intrinsically multi-configurational, and should be treated as such. One (very crude) way to try to understand it qualitatively is to treat it as a set of two weakly interacting Hueckel systems. One of the two corresponds to the familiar \pi system. It has five levels - a2", e1", and e2" (unless I misread the character tables) - and five electrons distributed in them. The ground electronic state of this subsystem would have doublet E1" symmetry[*] - degenerate both in spin and space. The second Hueckel system is formed by the five in-plane sp2-hybridized orbitals, pointing outwards (where hydrogens would have been in C5H5). The corresponding Hueckel MOs should be a1', e1', and e2' - so the ground state should be doublet E1' symmetry[+]. Now the interaction between these two subsystems should give you a set of six states - A1", A2", and E2", each coming in the singlet and the triplet flavour. Because the two Hueckel systems should be very weakly interacting because of the spatial separation, these states will appear very close to each other, with the triplet-E2" state likely being the lowest one[#]. Depending on the starting guess, your Sz=0 UHF solution (which is incapable of reproduing either the spatial or the spin symmetry of the correct answer) could converge to an arbitrarily crazy linear combination of these eight sublevels. To make things even more complicated, this model is excessively simplified already. For a more reasonable description, one would have to consider two more interacting Hueckel pairs: four electrons in the five pi orbitals interacting with six electrons in the sigma ring, and the symmetric combination of four electron in the sigma ring and six in the pi ring. The "true" ground-state solution may include contributions from these coonfigurations as well. The bottom line is that the minimally sensible way of looking at this system is to use a multi-configurational anzatz, with the absolute minimum of six electrons distributed over the four orbitals corresponding to the spatially-degenerate HOMOs of the two (pi and sigma) Hueckel subystems. It would also be possible to extract the state energies from a set of sufficiently cleverly chosen fractionally-occupied single-determinantal wavefunctions (the delta-SCF approach). Unless you are restricted to using single-determinantal approach - e.g. because you system is too large, and can only be handled by DFT - this is not something to be recommended. Have fun, Serguei [*] could be E2" if I mistread the tables [+] ditto [#] it is highly unlikely that the D5h structure is a local minimum on the PES for any of these states. On Thu, 10 Sep 2009, Steve Williams willsd|appstate.edu wrote: > > Sent to CCL by: Steve Williams [willsd-x-appstate.edu] > As part of a larger project I think I kneed to understand the electronic > properties of a hypothetical molecule: C5 in pentagonal (D5h) symmetry. I > know that the linear form of this molecule is known, and a C2V cyclic > structure has been investigated as well, but I want the pentagonal symmetry > ring form. After not understanding some more complex calculations I decided > to look at the basics: Hartree-Fock with sto-3g basis. Stable calculations in > G03 indicate that the rhf wavefunction is unstable with respect to a uhf > wavefunction. [rest deleted] --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 Skype: Serguei.Patchkovskii E-mail: Serguei.Patchkovskii^-^nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From owner-chemistry@ccl.net Thu Sep 10 20:10:00 2009 From: "Wolf-D.Ihlenfeldt wdi^^xemistry.com" To: CCL Subject: CCL: exhaustive tautomer generation Message-Id: <-40217-090910180539-3246-46SE5f8Q5QZTUXYuIMsitw .. server.ccl.net> X-Original-From: "Wolf-D.Ihlenfeldt" Content-Language: en-us Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="windows-1257" Date: Thu, 10 Sep 2009 22:51:19 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D.Ihlenfeldt" [wdi[*]xemistry.com] >=20 >=20 > Sent to CCL by: "Christian Pilger" [christian.pilger[a]gmx.net] > Dear CCLers, >=20 > For one of my projects I need to generate all possible tautomers for a > large set of structures. Which software packages are capable of > performing this task? Any hints are very welcome. Cactvs. See for example=20 The Impact of Tautomer Forms on Pharmacophore-Based Virtual Screening=86 Frank Oellien,=87 Jo=8Drg Cramer,=87 Carsten Beyer,=87,| Wolf-Dietrich = Ihlenfeldt,=A7 and Paul M. Selzer*,=87 >=20 > Cheers, >=20 > Christian >=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>=20>=20 From owner-chemistry@ccl.net Thu Sep 10 20:51:01 2009 From: "Antony Williams tony*chemspider.com" To: CCL Subject: CCL: CAS number to Smile String Message-Id: <-40218-090910204835-19963-lAYADWMKX57yRq13EUle9A^^^server.ccl.net> X-Original-From: "Antony Williams" Content-class: urn:content-classes:message Content-Type: multipart/related; boundary="----_=_NextPart_001_01CA3274.5E597208"; type="multipart/alternative" Date: Thu, 10 Sep 2009 20:11:12 -0400 MIME-Version: 1.0 Sent to CCL by: "Antony Williams" [tony[]chemspider.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01CA3274.5E597208 Content-Type: multipart/alternative; boundary="----_=_NextPart_002_01CA3274.5E597208" ------_=_NextPart_002_01CA3274.5E597208 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable There are a series of ChemSPider web services to use if you wish to avail yourself of them. The services are listed online here:=20 http://www.chemspider.com/Search.asmx =20 In terms of internet-based quality there are significant issues when it comes to registry numbers. For example, take a simple element like Carbon. CAS's own website declares the CAS registry number as 7440-44-0: http://www.commonchemistry.org/search.aspx?terms=3Dcarbon =20 A search on PubChem will give two hits: methane and progesterone:=20 http://www.ncbi.nlm.nih.gov/sites/entrez?db=3Dpccompound&term=3D7440-44-0= =20 Some of these issues have proliferated into databases utilizing PubChem as the seed set so a search on the NCI database also gives methane:=20 http://cactus.nci.nih.gov/chemical/structure/7440-44-0/file?format=3Dsdf = =20 There is no easy way to curate and validate CAS registry numbers as it requires access to the CAS Registry to validate so only investigative work and diligence can improve this situation and the majority of databases are not resourced to curate the data. It is also not allowable to use SciFinder to validate Registry Numbers as stated here=20 http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/CAS_va lidation=20 =20 Those databases with the resources and mission to curate do get it right and I recommend ChEBI as an example:=20 http://www.ebi.ac.uk/ebisearch/search.ebi?db=3DsmallMolecules&t=3D7440-44= -0 =20 Please note that many of the identifiers in ChemSPider, including CAS numbers, have been curated and validated by curators and by the public (crowdsourced curation). While the database is far from perfect we have put considerable effort into validating the data. =20 Feel free to contact us if you need help. =20 Antony Williams, VP Strategic Development ChemSpider, Royal Society of Chemistry US Office: 904 Tamaras Circle, Wake Forest, NC-27587 =20 Phone: +1 (919) 201-1516 Fax: +1 (919) 300-5321 =20 > From: owner-chemistry+wdi=3D=3Dxemistry.com-,-ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com-,-ccl.net] On Behalf Of Rajarshi Guha rajarshi.guha+*+gmail.com Sent: Thursday, September 10, 2009 7:30 PM To: Ihlenfeldt, Wolf D=20 Subject: CCL: CAS number to Smile String =20 =20 On Thu, Sep 10, 2009 at 12:27 PM, Chunhui Li baotogo2004#,#gmail.com < owner-chemistry]=3Dcl.net> wrote: Sent to CCL by: "Chunhui Li" [baotogo2004_._gmail.com] Hi Dear ALl, I want to generate smile strings for more than 100 chemicals. All I have is the CAS number for each chemical. Is there any tools I can use to do this automatically? One way to get it is to use the PubChem synonym tables - this is obviously not a comprehensive solution as it doesn't contain the entire CAS registry. There's a simple REST interface (based on a mirror of PubChem at IU). For example, given a CAS for aspirin visit http://toposome.chemistry.drexel.edu/~rguha/rest/db/pubchem/cas2smi/69-4 6-5 and you get back the SMILES for it. In general, replace the CAS at the end of the URL to whatever you want --=20 Rajarshi Guha NIH Chemical Genomics Center ------_=_NextPart_002_01CA3274.5E597208 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

There are a series of ChemSPider web services to use if = you wish to avail yourself of them. The services are listed online here: http://www.chemspider.com/= Search.asmx

In terms of internet-based quality there are significant = issues when it comes to registry numbers. For example, take a simple element = like Carbon. CAS’s own website declares the CAS registry number as = 7440-44-0: http:/= /www.commonchemistry.org/search.aspx?terms=3Dcarbon=

A search on PubChem will give two hits: methane and = progesterone: http://www.ncbi.nlm.nih.gov/sites/entrez?db=3Dpccompound&am= p;term=3D7440-44-0

Some of these issues have proliferated into databases = utilizing PubChem as the seed set so a search on the NCI database also gives = methane: http://cactus.nci.nih.gov/chemical/structure/7440-44-0/file?form= at=3Dsdf

There is no easy way to curate and validate CAS registry = numbers as it requires access to the CAS Registry to validate so only = investigative work and diligence can improve this situation and the majority of = databases are not resourced to curate the data. It is also not allowable to use = SciFinder to validate Registry Numbers as stated here http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_= Chemistry/CAS_validation

Those databases with the resources and mission to curate = do get it right and I recommend ChEBI as an example: http://www.ebi.ac.uk/ebisearch/search.ebi?db=3DsmallMolec= ules&t=3D7440-44-0

Please note that many of the identifiers in ChemSPider, = including CAS numbers, have been curated and validated by curators and by the = public (crowdsourced curation). While the database is far from perfect we have put = considerable effort into validating the data.

Feel free to contact us if you need = help.

= Antony Williams, VP Strategic Development

ChemSpider, Royal Society = of Chemistry

US Office: 904 Tamaras Circle, Wake Forest, = NC-27587

Phone: +1 (919) 201-1516
Fax: +1 (919) 300-5321

From:= owner-chemistry+wdi=3D=3Dxemistry.com-,-ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com-,-ccl.net] On Behalf Of = Rajarshi Guha rajarshi.guha+*+gmail.com
Sent: Thursday, September 10, 2009 7:30 PM
To: Ihlenfeldt, Wolf D
Subject: CCL: CAS number to Smile String

On Thu, Sep 10, 2009 at 12:27 PM, Chunhui Li = baotogo2004#,#gmail.com <owner-chemistry]=3Dcl.net&g= t; wrote:

--
Rajarshi Guha
NIH Chemical Genomics Center

------_=_NextPart_002_01CA3274.5E597208-- ------_=_NextPart_001_01CA3274.5E597208 Content-Type: image/png; name="image001.png" Content-Transfer-Encoding: base64 Content-ID: Content-Description: image001.png Content-Location: image001.png iVBORw0KGgoAAAANSUhEUgAAAIYAAACGCAMAAAAvpwKjAAAAAXNSR0ICQMB9xQAAAANQTFRFAAAA p3o92gAAAAF0Uk5TAEDm2GYAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAAZdEVYdFNvZnR3YXJlAE1p Y3Jvc29mdCBPZmZpY2V/7TVxAAAAKElEQVR42u3BgQAAAADDoPlT3+AEVQEAAAAAAAAAAAAAAAAA AAAAwDNGqgAB7T8OeAAAAABJRU5ErkJggg== ------_=_NextPart_001_01CA3274.5E597208-- From owner-chemistry@ccl.net Thu Sep 10 21:25:01 2009 From: "Andrew Orry andy .. molsoft.com" To: CCL Subject: CCL: exhaustive tautomer generation Message-Id: <-40219-090910211703-8319-+m1ecpn6xlSAAH9JpGHqwA|-|server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 10 Sep 2009 18:13:03 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy-x-molsoft.com] MolSoft's ICM-Chemist software can generate all possible tautomers interactively or in batch mode. See http://www.molsoft.com/icm-chemist.html for more information. Thanks, Andy -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com Latest ICM News: www.molsoft.com/news.html Christian Pilger christian.pilger]~[gmx.net wrote: > Sent to CCL by: "Christian Pilger" [christian.pilger[a]gmx.net] > Dear CCLers, > > For one of my projects I need to generate all possible tautomers for a large set of structures. Which software packages are capable of performing this task? Any hints are very welcome. > > Cheers, > > Christian> >