From owner-chemistry@ccl.net Thu Jun 10 01:50:00 2010
From: "Gerard Pujadas gerard.pujadas.:.gmail.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: How to perform an "Exact structure search" into eMolecules (or similar database) by using a large list of SMILES
Message-Id: <-42079-100609201854-6965-CmF2jIwuX2bb64/HLKUT0Q[A]server.ccl.net>
X-Original-From: Gerard Pujadas <gerard.pujadas!=!gmail.com>
Content-Type: multipart/alternative; boundary=0016e6d9990f2e5d210488a108c3
Date: Thu, 10 Jun 2010 01:11:55 +0200
MIME-Version: 1.0


Sent to CCL by: Gerard Pujadas [gerard.pujadas- -gmail.com]

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Content-Type: text/plain; charset=ISO-8859-1

Dear CCL list members,

we have a database with around 100.000 molecules and we would like to
include a field for each molecule that reports (if any) the different
commercial suppliers that sell it. I have found that eMolecules (
http://www.emolecules.com/) could provided me with that information but the
problem is that the "Exact structure search" option seems to be available
only when you draw the structure in their structure editor and not when you
use the smiles as a search criteria ... For instance I have searched for
commercial suppliers of one of our favorite molecules (*i.e.* *
C1C(=O)NC2=C(S1)C=C(C=C2)Cl*) but the problem is that this search results in
two molecules (the first one is the one I want and the second one is a
derivative of the former). This is not a problem when you search a single
molecule but it is important when you are searching for hundreds of
molecules and want to implement one script that can do that job
automatically ...

Thus my question is about how to perform a "Exact structure search" with
eMolecules by using, exclusively, a list with the smiles of my molecules.

Please, if the requested job can be run with a server different than
eMolecules,
please, let me know also.

Do not hesitate to contact me if you need further information

With many thanks in advances for your help

Best

Gerard

-- 
Gerard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=22
Nutrigenomics Research Group
phone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Universitat Rovira i Virgili
Tarragona, Catalonia

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Dear <span class=3D"il">CCL list members</span>,<br><br>we have a database =
with around 100.000 molecules and we would like to include a field for each=
 molecule that reports (if any) the different commercial suppliers that sel=
l it. I have found that <span class=3D"il">eMolecules (<a href=3D"http://ww=
w.emolecules.com/">http://www.emolecules.com/</a>)</span> could provided me=
 with that information but the problem is that the &quot;Exact structure se=
arch&quot; option seems to be available only when you draw the structure in=
 their structure editor and not when you use the smiles as a search criteri=
a ... For instance I have searched for commercial=20
suppliers of one of our favorite molecules (<i>i.e.</i> <b>C1C(=3DO)NC2=3DC=
(S1)C=3DC(C=3DC2)Cl</b>)
 but the problem is that this search results in two molecules (the first
 one is the one I want and the second one is a derivative of the former). T=
his is not a problem when you search a=20
single molecule but it is important when you are searching for hundreds=20
of molecules and want to implement one script that can do that job automati=
cally ...<br><br>Thus my question is about how to perform a &quot;Exact str=
ucture search&quot; with eMolecules by using, exclusively, a list with the =
smiles of my molecules.<br>
<br>Please, if the requested job can be run with a server different than <s=
pan class=3D"il">eMolecules, please, let me know also.</span><br><br>Do not=
 hesitate to contact me if you need further=20
information<br><br>With many thanks in advances for your help<br><br>Best<b=
r><br>Gerard<br clear=3D"all"><br>-- <br>Gerard Pujadas<br><a href=3D"http:=
//bioquimica.urv.cat/eng/fitxa.jsp?id=3D22">http://bioquimica.urv.cat/eng/f=
itxa.jsp?id=3D22</a><br>
Nutrigenomics Research Group<br>phone +34 977 55 (9565)<br>Biochemistry and=
 Biotechnology Department<br>Universitat Rovira i Virgili<br>Tarragona, Cat=
alonia<br>

--0016e6d9990f2e5d210488a108c3--


From owner-chemistry@ccl.net Thu Jun 10 05:16:00 2010
From: "Serge Dom serge.dom()gmail.com" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL:G: minimum energy path calculation
Message-Id: <-42080-100610043608-3961-BZNY1F09iO8DJay163o3zA-$-server.ccl.net>
X-Original-From: Serge Dom <serge.dom .. gmail.com>
Content-Type: multipart/alternative; boundary=00032555aa1249fb600488a8809e
Date: Thu, 10 Jun 2010 11:06:35 +0300
MIME-Version: 1.0


Sent to CCL by: Serge Dom [serge.dom|-|gmail.com]
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Content-Type: text/plain; charset=ISO-8859-1

 Hello,

I have to do minimum energy path calculation which connect reactant and
product of the reaction which was located using DFT calculation with g03
program. Which programs can I used for minimum energy path calculations?
Unfortunately I have never done such type of calculations before and have no
ideas how to start it. Examples of the calculations or references for such
calculations will be very welcome.

Thank you in advance  Serge

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<div dir=3D"ltr"><div class=3D"gmail_quote">
<div dir=3D"ltr">
<div>Hello,</div>
<div>=A0</div>
<div>I have to do minimum energy path calculation which connect=A0reactant =
and product of the reaction=A0which was located using DFT calculation with =
g03 program. Which programs can I used for minimum energy path calculations=
? Unfortunately I have=A0never done such type of calculations before and ha=
ve no ideas how to start it. Examples of the calculations or references for=
 such calculations will be very welcome.</div>

<div>=A0</div>
<div>Thank you in advance=A0 Serge</div></div></div><br></div>

--00032555aa1249fb600488a8809e--


From owner-chemistry@ccl.net Thu Jun 10 06:07:00 2010
From: "Esteban Gabriel Vega Hissi egvega[*]gmail.com" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL:G: minimum energy path calculation
Message-Id: <-42081-100610060359-13065-76w2RgC8ocF9vzF4/vXxYQ]![server.ccl.net>
X-Original-From: Esteban Gabriel Vega Hissi <egvega__gmail.com>
Content-Type: multipart/alternative; boundary=0016368334128e1bf70488aa2378
Date: Thu, 10 Jun 2010 12:03:29 +0200
MIME-Version: 1.0


Sent to CCL by: Esteban Gabriel Vega Hissi [egvega .. gmail.com]
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Content-Type: text/plain; charset=ISO-8859-1

Hi,
You should do IRC calculations, check Gaussian manual

Esteban
UNSL
Argetina

--

On Thu, Jun 10, 2010 at 10:06 AM, Serge Dom serge.dom()gmail.com <
owner-chemistry=ccl.net> wrote:

>  Hello,
>
> I have to do minimum energy path calculation which connect reactant and
> product of the reaction which was located using DFT calculation with g03
> program. Which programs can I used for minimum energy path calculations?
> Unfortunately I have never done such type of calculations before and have no
> ideas how to start it. Examples of the calculations or references for such
> calculations will be very welcome.
>
> Thank you in advance  Serge
>
>

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Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Hi,<br>You should do IRC calculations, check Gaussian manual<br><br>Esteban=
<br>UNSL<br>Argetina<br><br>--<br><br><div class=3D"gmail_quote">On Thu, Ju=
n 10, 2010 at 10:06 AM, Serge Dom serge.dom()<a href=3D"http://gmail.com">g=
mail.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry=ccl.ne=
t">owner-chemistry=ccl.net</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir=3D"ltr">=
<div class=3D"gmail_quote">
<div dir=3D"ltr">
<div>Hello,</div>
<div>=A0</div>
<div>I have to do minimum energy path calculation which connect=A0reactant =
and product of the reaction=A0which was located using DFT calculation with =
g03 program. Which programs can I used for minimum energy path calculations=
? Unfortunately I have=A0never done such type of calculations before and ha=
ve no ideas how to start it. Examples of the calculations or references for=
 such calculations will be very welcome.</div>



<div>=A0</div>
<div>Thank you in advance=A0 Serge</div></div></div><br></div>
</blockquote></div><br>

--0016368334128e1bf70488aa2378--


From owner-chemistry@ccl.net Thu Jun 10 07:31:01 2010
From: "partha pratim kundu partha1kundu * yahoo.com" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL:G: GAR2PED
Message-Id: <-42082-100610072858-10586-D8BDHbpVel+OanK1CUvgGg/a\server.ccl.net>
X-Original-From: "partha  pratim kundu" <partha1kundu/a\yahoo.com>
Date: Thu, 10 Jun 2010 07:28:57 -0400


Sent to CCL by: "partha  pratim kundu" [partha1kundu|yahoo.com]
Dear Zborowsk,
After replacing my Gaussian log file all '|' & '/' with '\' pullarc is working fine and it is creating two files .arch and .xyz. But if I type gar2ped.x file_name it is saying

archive record contains Z-matrix rather than
 Cartesian coordinates --- reading from .xyz file
open: No such file or directory
apparent state: unit 69 named BENZ2.xyz
last format: list io
lately writing sequential formatted external IO
Aborted

This happens with the file that you have sent me also. (Strangely first time it gave me some output  apt.xyz but not other extension files, also saying it contains z-matrix).

Have you tried gar2ped keyword with your archive file?

regards.
Partha.


From owner-chemistry@ccl.net Thu Jun 10 08:06:00 2010
From: "Thomas Gkourmpis thomas.gkourmpis*borealisgroup.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL:G: minimum energy path calculation
Message-Id: <-42083-100610072831-9876-ozpQPf2HSyyzuzE0tQK06w : server.ccl.net>
X-Original-From: "Thomas  Gkourmpis" <thomas.gkourmpis*o*borealisgroup.com>
Date: Thu, 10 Jun 2010 07:28:30 -0400


Sent to CCL by: "Thomas  Gkourmpis" [thomas.gkourmpis[a]borealisgroup.com]
You need to perform an IRC (intrinsic reaction coordinate) search, giving the TS as an input. In the options you can define how many steps you want on each direction (i.e. forward towards the products and backwards towards the reactants) and after that you are good to go. Depending on the software package youre using different keyword options are available, but I assume theyre explained in detail in the manual.

I hope that helped

Thomas


> "Serge Dom serge.dom()gmail.com"  wrote:
> 
> Sent to CCL by: Serge Dom [serge.dom|-|gmail.com]
> --00032555aa1249fb600488a8809e
> Content-Type: text/plain; charset=ISO-8859-1
> 
>  Hello,
> 
> I have to do minimum energy path calculation which connect reactant and
> product of the reaction which was located using DFT calculation with g03
> program. Which programs can I used for minimum energy path calculations?
> Unfortunately I have never done such type of calculations before and have no
> ideas how to start it. Examples of the calculations or references for such
> calculations will be very welcome.
> 
> Thank you in advance  Serge
> 
> --00032555aa1249fb600488a8809e
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> 
> <div dir=3D"ltr"><div class=3D"gmail_quote">
> <div dir=3D"ltr">
> <div>Hello,</div>
> <div>=A0</div>
> <div>I have to do minimum energy path calculation which connect=A0reactant =
> and product of the reaction=A0which was located using DFT calculation with =
> g03 program. Which programs can I used for minimum energy path calculations=
> ? Unfortunately I have=A0never done such type of calculations before and ha=
> ve no ideas how to start it. Examples of the calculations or references for=
>  such calculations will be very welcome.</div>
> 
> <div>=A0</div>
> <div>Thank you in advance=A0 Serge</div></div></div><br></div>
> 
> --00032555aa1249fb600488a8809e--
> 
>


From owner-chemistry@ccl.net Thu Jun 10 08:41:01 2010
From: "Serdar Bado?lu sbadoglu.*|*.gazi.edu.tr" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: tautomer ratios
Message-Id: <-42084-100610065801-27076-jbak9LPGpz8SBICWNxwoyQ*|*server.ccl.net>
X-Original-From: "Serdar Bado?lu" <sbadoglu#,#gazi.edu.tr>
Date: Thu, 10 Jun 2010 10:02:21 -0000


Sent to CCL by: "Serdar Bado?lu" [sbadoglu * gazi.edu.tr]
Hi all,

I have computed the Gibbs free energy difference between the tautomers and
then by using the Boltzmann distribution to get the ratio. I have tested
this method on some papers, and it worked well. Unfortunately, in my
situation it failed. A previous paper reported the raio as 7 : 3 from the
NMR (in heavy water) experiment, but my calculation gave a 5.1 : 4.9
ratio. My calculation level is B3LYP / 6-311++G** and the solvent effect
is included. I suppose experimental and theoretical results are
inconsistent in this case. I'm trying to figure out what can be the cause
of this discrepancy.

Any ideas?

Regards


-- 
Serdar BADOGLU
Gazi University
Department of Physics


From owner-chemistry@ccl.net Thu Jun 10 09:16:00 2010
From: "Chris Swain swain%mac.com" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL: How to perform an "Exact structure search" into eMolecules (or similar database) by using a large list of SMILES
Message-Id: <-42085-100610080941-10910-cIJXanajna8XTEPZRTYTjQ~!~server.ccl.net>
X-Original-From: Chris Swain <swain:_:mac.com>
Content-type: multipart/alternative;
 boundary="Boundary_(ID_oM3me1u3KuE+cHd0UACu7A)"
Date: Thu, 10 Jun 2010 12:09:26 +0100
MIME-version: 1.0


Sent to CCL by: Chris Swain [swain]*[mac.com]

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Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
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Hi,

I don't know about eMolecules, but I did a similar thing by  
downloading the ZINC dataset (http://zinc.docking.org/) then used  
Openbabel to do the searching.

Chris

On 10 Jun 2010, at 00:11, Gerard Pujadas gerard.pujadas.:.gmail.com  
wrote:

> Dear CCL list members,
>
> we have a database with around 100.000 molecules and we would like  
> to include a field for each molecule that reports (if any) the  
> different commercial suppliers that sell it. I have found that  
> eMolecules (http://www.emolecules.com/) could provided me with that  
> information but the problem is that the "Exact structure search"  
> option seems to be available only when you draw the structure in  
> their structure editor and not when you use the smiles as a search  
> criteria ... For instance I have searched for commercial suppliers  
> of one of our favorite molecules (i.e. C1C(=O)NC2=C(S1)C=C(C=C2)Cl)  
> but the problem is that this search results in two molecules (the  
> first one is the one I want and the second one is a derivative of  
> the former). This is not a problem when you search a single molecule  
> but it is important when you are searching for hundreds of molecules  
> and want to implement one script that can do that job  
> automatically ...
>
> Thus my question is about how to perform a "Exact structure search"  
> with eMolecules by using, exclusively, a list with the smiles of my  
> molecules.
>
> Please, if the requested job can be run with a server different than  
> eMolecules, please, let me know also.
>
> Do not hesitate to contact me if you need further information
>
> With many thanks in advances for your help
>
> Best
>
> Gerard
>
> -- 
> Gerard Pujadas
> http://bioquimica.urv.cat/eng/fitxa.jsp?id=22
> Nutrigenomics Research Group
> phone +34 977 55 (9565)
> Biochemistry and Biotechnology Department
> Universitat Rovira i Virgili
> Tarragona, Catalonia


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<html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; ">Hi,<div><br></div><div>I don't =
know about eMolecules, but I did a similar thing by downloading the ZINC =
dataset (<a =
href=3D"http://zinc.docking.org/">http://zinc.docking.org/</a>) then =
used Openbabel to do the =
searching.</div><div><br></div><div>Chris</div><div><br><div><div>On 10 =
Jun 2010, at 00:11, Gerard Pujadas gerard.pujadas.:.gmail.com =
wrote:</div><br class=3D"Apple-interchange-newline"><blockquote =
type=3D"cite">Dear <span class=3D"il">CCL list members</span>,<br><br>we =
have a database with around 100.000 molecules and we would like to =
include a field for each molecule that reports (if any) the different =
commercial suppliers that sell it. I have found that <span =
class=3D"il">eMolecules (<a =
href=3D"http://www.emolecules.com/">http://www.emolecules.com/</a>)</span>=
 could provided me with that information but the problem is that the =
"Exact structure search" option seems to be available only when you draw =
the structure in their structure editor and not when you use the smiles =
as a search criteria ... For instance I have searched for commercial =
suppliers of one of our favorite molecules (<i>i.e.</i> =
<b>C1C(=3DO)NC2=3DC(S1)C=3DC(C=3DC2)Cl</b>) but the problem is that this =
search results in two molecules (the first one is the one I want and the =
second one is a derivative of the former). This is not a problem when =
you search a single molecule but it is important when you are searching =
for hundreds of molecules and want to implement one script that can do =
that job automatically ...<br><br>Thus my question is about how to =
perform a "Exact structure search" with eMolecules by using, =
exclusively, a list with the smiles of my molecules.<br> <br>Please, if =
the requested job can be run with a server different than <span =
class=3D"il">eMolecules, please, let me know also.</span><br><br>Do not =
hesitate to contact me if you need further information<br><br>With many =
thanks in advances for your help<br><br>Best<br><br>Gerard<br =
clear=3D"all"><br>-- <br>Gerard Pujadas<br><a =
href=3D"http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22">http://bioquimica=
.urv.cat/eng/fitxa.jsp?id=3D22</a><br> Nutrigenomics Research =
Group<br>phone +34 977 55 (9565)<br>Biochemistry and Biotechnology =
Department<br>Universitat Rovira i Virgili<br>Tarragona, =
Catalonia<br></blockquote></div><br></div></body></html>=

--Boundary_(ID_oM3me1u3KuE+cHd0UACu7A)--


From owner-chemistry@ccl.net Thu Jun 10 11:45:00 2010
From: "Upakarasamy Lourderaj u.lourderaj^-^gmail.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: PBC with gaussian
Message-Id: <-42086-100610080107-4457-d3jRwebDKMPwr3DYJMgDWQ++server.ccl.net>
X-Original-From: "Upakarasamy  Lourderaj" <u.lourderaj%gmail.com>
Date: Thu, 10 Jun 2010 08:01:06 -0400


Sent to CCL by: "Upakarasamy  Lourderaj" [u.lourderaj!^!gmail.com]
I am studying interaction of organic molecules on surfaces.  I would appreciate very much if you let me guide through as to how to give input for such calculations. I want to use periodic boundary condition(PBC) for the surface only, while the organic molecule should treated as a single molecule.  Can we do such calculations using g03?


From owner-chemistry@ccl.net Thu Jun 10 12:20:00 2010
From: "vadiraj kurdekar vadirajgcppc^^^yahoo.co.in" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: how to select decoys
Message-Id: <-42087-100610090600-27821-4lyz0IBpZeA9BL59XgYnyQ-$-server.ccl.net>
X-Original-From: vadiraj kurdekar <vadirajgcppc[]yahoo.co.in>
Content-Type: multipart/alternative; boundary="0-709880418-1276171548=:39395"
Date: Thu, 10 Jun 2010 17:35:48 +0530 (IST)
MIME-Version: 1.0


Sent to CCL by: vadiraj kurdekar [vadirajgcppc|a|yahoo.co.in]
--0-709880418-1276171548=:39395
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable


hello to all
=A0
I would like to=A0validate query created in ROCS (Openeye) for=A0MMP13 inhi=
bitor i have set of=A0compounds (nearly 1,100) in nanoMolar to milliMolar r=
ange=A0active compounds from literature, but my query is=20
1). how to select decoys=A0and actives from this database. what will be cut=
off value ?=20
2).=A0should i select decoys form other source if so what should be the cri=
teria ?
4). how i=A0will come to know selected decoys are inactive ?
3). as decoys are physicochemically similar to actives what happens if deco=
ys are docked to given target ?
4). is there any program to create decoys which are similar to given molecu=
le ?
=A0
Thanks in advance.

With Regards,
=A0


Vadiraj Kurdekar,
Research Scholar,=20
Pharmacy group,
Birla Institute of Technology and Science-Pilani,
Rajasthan,
India.
Mobile: + 91 9460763664
email: vadirajgcppc[-]yahoo.co.in


This e-mail (and any attachments), is confidential and may be privileged. I=
t may be read, copied and used only by intended recipients. Unauthorized ac=
cess to this e-mail (or attachments) and disclosure or copying of its conte=
nts or any action taken in reliance on it is unlawful. Unintended recipient=
s must notify the sender immediately by e-mail/phone & delete it from their=
 system without making any copies or disclosing it to a third person.

=0A=0A
--0-709880418-1276171548=:39395
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;"><DIV><BR>hello to all</DIV>
<DIV>&nbsp;</DIV>
<DIV>I would like to&nbsp;validate query created in ROCS (Openeye) for&nbsp=
;MMP13 inhibitor i have set of&nbsp;compounds (nearly 1,100) in nanoMolar t=
o milliMolar range&nbsp;active compounds from literature, but my query is <=
/DIV>
<DIV>1). how to select decoys&nbsp;and actives from this database. what wil=
l be cutoff value ? </DIV>
<DIV>2).&nbsp;should i select decoys form other source if so what should be=
 the criteria ?</DIV>
<DIV>4). how i&nbsp;will come to know selected decoys are inactive ?</DIV>
<DIV>3). as decoys are physicochemically similar to actives what happens if=
 decoys are docked to given target ?</DIV>
<DIV>4). is there any program to create decoys which are similar to given m=
olecule ?</DIV>
<DIV>&nbsp;</DIV>
<DIV>Thanks in advance.<BR><BR><STRONG><EM><FONT color=3D#00bf60 size=3D2 f=
ace=3D"arial, helvetica, sans-serif">With Regards,</FONT></EM></STRONG></DI=
V>
<DIV><STRONG><EM><FONT color=3D#00bf60 size=3D4 face=3DArial></FONT></EM></=
STRONG>&nbsp;</DIV>
<DIV><FONT color=3D#0000ff><FONT face=3D"arial, helvetica, sans-serif"><STR=
ONG></STRONG></FONT></FONT></DIV>
<DIV><FONT color=3D#0000ff><FONT face=3D"arial, helvetica, sans-serif"><STR=
ONG></STRONG></FONT></FONT></DIV>
<DIV><FONT color=3D#c00000 size=3D2 face=3D"verdana, helvetica, sans-serif"=
><STRONG><SPAN>Vadiraj</SPAN> Kurdekar,</STRONG></FONT></DIV>
<DIV><FONT color=3D#0000ff size=3D2 face=3D"verdana, helvetica, sans-serif"=
>Research Scholar, </FONT></DIV>
<DIV><FONT color=3D#0000ff size=3D2 face=3D"verdana, helvetica, sans-serif"=
>Pharmacy group,</FONT></DIV>
<DIV><A href=3D"http://www.bits-pilani.ac.in/" rel=3Dnofollow target=3D_bla=
nk><FONT color=3D#0000ff size=3D2 face=3D"verdana, helvetica, sans-serif">B=
irla Institute of Technology and Science-Pilani,</FONT></A></DIV>
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--0-709880418-1276171548=:39395--


From owner-chemistry@ccl.net Thu Jun 10 12:54:00 2010
From: "John McKelvey jmmckel|a|gmail.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Many cis-trans possible configurations
Message-Id: <-42088-100610113629-4056-OxsH9j4H2lwWjHfGhppXfA+*+server.ccl.net>
X-Original-From: John McKelvey <jmmckel,gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 10 Jun 2010 09:42:36 -0400
MIME-Version: 1.0


Sent to CCL by: John McKelvey [jmmckel**gmail.com]
Hello,

For molecules with several, say 3 or 4, floppy conjugated bonds is
there any code that will sample all possible cis-trans configurations
and report the lowest energy one?

Thanks,

John

-- 
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel(-)gmail.com


From owner-chemistry@ccl.net Thu Jun 10 13:29:00 2010
From: "Barry Hardy barry.hardy+/-vtxmail.ch" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: Advancing Predictive Toxicology Strategies and Infrastructure
Message-Id: <-42089-100610113321-2487-nWUALUuaPCE7Nq3Tugz3ZQ|server.ccl.net>
X-Original-From: Barry Hardy <barry.hardy-$-vtxmail.ch>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
Date: Thu, 10 Jun 2010 17:02:45 +0200
MIME-Version: 1.0


Sent to CCL by: Barry Hardy [barry.hardy(0)vtxmail.ch]

We have had a lot of activity in recent months on the OpenTox project 
with regards to developing a linked data and resource infrastructure for 
the support of interdisciplinary predictive toxicology research and 
safety assessment.  I enclose several links below including our recent 
overview workshop presentation in Potsdam, reports, demonstrations, 
technical links and interest groups.  A paper will be published as an 
Open Access publication in coming weeks (reference below).

best regards
Barry Hardy
OpenTox Project Coordinator (www.opentox.org)

Connecting Your Resources to OpenTox and Other Connected Resources
This is an expanding community effort and we welcome your involvement!
If you have a useful resource you would like to see integrated into 
OpenTox, e.g., a database, bioinformatics tool, computational chemistry 
program etc., please contact me to discuss.We especially welcome high 
quality Open Source programs providing a valuable service to users.

OpenTox Presentation on Integrating Predictive Toxicology Resources
Potsdam, 30 May 2010
OpenTox Presentation:
http://www.opentox.org/home/documents/presentations/opentoxpresPotsdam30May2010/view
Program:
http://www.opentox.org/data/blogentries/public/opentoxworkshoppotsdam2010

Strategies
http://barryhardy.blogs.com/theferryman/2010/05/developing-new-predictive-toxicology-strategies.html

OpenTox Reports (Open Access)
http://www.opentox.org/home/documents/Reports

OpenTox Demos (Open to all to Try!)
(Please keep in mind these are early prototype applications and may not 
have features you want.  We welcome requests from you for what you 
additionally need in these applications or others.)
http://www.opentox.org/toxicity-prediction

OpenTox Signup & Mailing List
Complete the form at http://www.opentox.org/join_form
Note: If you have a general interest and want to receive a monthly news 
update e.g., on new applications, data resources, ontology developments, 
news etc., select the "I'm interested in OpenTox news"
option.  We also welcome including news from other projects in the 
newsletter.  Do not select the option "I'm interested in OpenTox 
Technical Development" unless you are doing technical computing work
in the field as this list is quite technical and busy!

OpenTox Collaboration Pool
If you are interested in joining virtual organisation collaborations in 
predictive toxicology supported by OpenTox, complete the form linked from:
http://www.opentox.org/data/blogentries/public/opentoxcollaborationpool

Technical Development Details including API (Open Access)
http://www.opentox.org/dev
http://www.opentox.org/dev/apis

Publication Reference (Open Access)
Collaborative Development of Predictive Toxicology Applications, B. 
Hardy, N. Douglas, C. Helma, M. Rautenberg, N. Jeliazkova, V. Jeliazkov, 
I. Nikolova, R. Benigni, O. Tcheremenskaia, S. Kramer, T. Girschick, F. 
Buchwald, J. Wicker, A. Karwath, M. Gütlein, A. Maunz, H. Sarimveis, G. 
Melagraki, A. Afantitis, P. Sopasakis, D. Gallagher, V. Poroikov, D. 
Filimonov, A. Zakharov, A. Lagunin, T. Gloriozova, S. Novikov, N. 
Skvortsova, D. Druzhilovsky , S. Chawla, I. Ghosh, S. Ray, H. Patel, S. 
Escher, accepted 3 June 2010 for Open Access publication in J. Chemical 
Informatics http://www.jcheminf.com/ (2010).


Barry Hardy PhD
Director, Community of Practice & Research Activities
and OpenTox Project Coordinator (www.opentox.org)
Douglas Connect
Baermeggenweg 14
4314 Zeiningen
Switzerland
Tel: +41 61 851 0170


From owner-chemistry@ccl.net Thu Jun 10 14:04:00 2010
From: "Wolf Ihlenfeldt wdi.:.xemistry.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: How to perform an "Exact structure search" into eMolecules (or similar database) by using a large list of SMILES
Message-Id: <-42090-100610111400-19015-ABslEkoNKgjVoi+l5LSOvw%a%server.ccl.net>
X-Original-From: Wolf Ihlenfeldt <wdi^xemistry.com>
Content-Type: multipart/alternative; boundary=0016e6d9a3acb127c50488ad9353
Date: Thu, 10 Jun 2010 15:09:55 +0100
MIME-Version: 1.0


Sent to CCL by: Wolf Ihlenfeldt [wdi(0)xemistry.com]
--0016e6d9a3acb127c50488ad9353
Content-Type: text/plain; charset=UTF-8

Easy enough to do with a simple Cactvs script (www.xemistry.com/academic,
free for academic users):

--- snip ---
molfile loop myfile.smi eh {
   if {[catch {ens get $eh E_EMOLECULES_URL} url]} {
    puts "No EMolecules data for [ens get $eh E_SMILES]"
  } else {
     puts "SMILES: [ens get $eh E_SMILES] EMolecules URL: $url"
  }
}
--- snip ---

Run with the generic interpreter (i.e. on Unix/Linux, use "csts -f
myscript.tcl"). With your test structure, only a single result is found,
since the query processor automatically uses molecular weight as an
additional criterion, which excludes the derivative.

Still, this hits the EMolecules site once for each structure. I am not sure
they will like that. You can buy their database for in-house use, and I am
certain this is what they would recommend for this type of use.

Running this will also take time to complete over the Internet - EMolecules
response times seem to be 2-3 secs per full-structure query.





On Thu, Jun 10, 2010 at 12:11 AM, Gerard Pujadas gerard.pujadas.:.gmail.com
<owner-chemistry[A]ccl.net> wrote:

> Dear CCL list members,
>
> we have a database with around 100.000 molecules and we would like to
> include a field for each molecule that reports (if any) the different
> commercial suppliers that sell it. I have found that eMolecules (
> http://www.emolecules.com/) could provided me with that information but
> the problem is that the "Exact structure search" option seems to be
> available only when you draw the structure in their structure editor and not
> when you use the smiles as a search criteria ... For instance I have
> searched for commercial suppliers of one of our favorite molecules (*i.e.*
> *C1C(=O)NC2=C(S1)C=C(C=C2)Cl*) but the problem is that this search results
> in two molecules (the first one is the one I want and the second one is a
> derivative of the former). This is not a problem when you search a single
> molecule but it is important when you are searching for hundreds of
> molecules and want to implement one script that can do that job
> automatically ...
>
> Thus my question is about how to perform a "Exact structure search" with
> eMolecules by using, exclusively, a list with the smiles of my molecules.
>
> Please, if the requested job can be run with a server different than eMolecules,
> please, let me know also.
>
> Do not hesitate to contact me if you need further information
>
> With many thanks in advances for your help
>
> Best
>
> Gerard
>
> --
> Gerard Pujadas
> http://bioquimica.urv.cat/eng/fitxa.jsp?id=22
> Nutrigenomics Research Group
> phone +34 977 55 (9565)
> Biochemistry and Biotechnology Department
> Universitat Rovira i Virgili
> Tarragona, Catalonia
>

--0016e6d9a3acb127c50488ad9353
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<br>Easy enough to do with a simple Cactvs script (<a href=3D"http://www.xe=
mistry.com/academic">www.xemistry.com/academic</a>, free for academic users=
):<br><br>--- snip ---<br>molfile loop myfile.smi eh {<br>=C2=A0=C2=A0 if {=
[catch {ens get $eh E_EMOLECULES_URL} url]} {<br>
=C2=A0=C2=A0=C2=A0 puts &quot;No EMolecules data for [ens get $eh E_SMILES]=
&quot;<br>=C2=A0 } else {<br>=C2=A0=C2=A0=C2=A0=C2=A0 puts &quot;SMILES: [e=
ns get $eh E_SMILES] EMolecules URL: $url&quot;<br>=C2=A0 }<br>}<br>--- sni=
p ---<br><br>Run with the generic interpreter (i.e. on Unix/Linux, use &quo=
t;csts -f myscript.tcl&quot;). With your test structure, only a single resu=
lt is found, since the query processor automatically uses molecular weight =
as an additional criterion, which excludes the derivative.<br>
<br>Still, this hits the EMolecules site once for each structure. I am not =
sure they will like that. You can buy their database for in-house use, and =
I am certain this is what they would recommend for this type of use. <br>
<br>Running this will also take time to complete over the Internet - EMolec=
ules response times seem to be 2-3 secs per full-structure query.<br><br><b=
r><br><br><br><div class=3D"gmail_quote">On Thu, Jun 10, 2010 at 12:11 AM, =
Gerard Pujadas gerard.pujadas.:.<a href=3D"http://gmail.com">gmail.com</a> =
<span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry[A]ccl.net">owner-chem=
istry[A]ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear <span>CCL li=
st members</span>,<br><br>we have a database with around 100.000 molecules =
and we would like to include a field for each molecule that reports (if any=
) the different commercial suppliers that sell it. I have found that <span>=
eMolecules (<a href=3D"http://www.emolecules.com/" target=3D"_blank">http:/=
/www.emolecules.com/</a>)</span> could provided me with that information bu=
t the problem is that the &quot;Exact structure search&quot; option seems t=
o be available only when you draw the structure in their structure editor a=
nd not when you use the smiles as a search criteria ... For instance I have=
 searched for commercial=20
suppliers of one of our favorite molecules (<i>i.e.</i> <b>C1C(=3DO)NC2=3DC=
(S1)C=3DC(C=3DC2)Cl</b>)
 but the problem is that this search results in two molecules (the first
 one is the one I want and the second one is a derivative of the former). T=
his is not a problem when you search a=20
single molecule but it is important when you are searching for hundreds=20
of molecules and want to implement one script that can do that job automati=
cally ...<br><br>Thus my question is about how to perform a &quot;Exact str=
ucture search&quot; with eMolecules by using, exclusively, a list with the =
smiles of my molecules.<br>

<br>Please, if the requested job can be run with a server different than <s=
pan>eMolecules, please, let me know also.</span><br><br>Do not hesitate to =
contact me if you need further=20
information<br><br>With many thanks in advances for your help<br><br>Best<b=
r><br>Gerard<br clear=3D"all"><font color=3D"#888888"><br>-- <br>Gerard Puj=
adas<br><a href=3D"http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22" target=
=3D"_blank">http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22</a><br>

Nutrigenomics Research Group<br>phone +34 977 55 (9565)<br>Biochemistry and=
 Biotechnology Department<br>Universitat Rovira i Virgili<br>Tarragona, Cat=
alonia<br>
</font></blockquote></div><br>

--0016e6d9a3acb127c50488ad9353--


From owner-chemistry@ccl.net Thu Jun 10 14:39:00 2010
From: "Ol Ga eurisco1(0)pochta.ru" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL:G: PBC with gaussian
Message-Id: <-42091-100610133953-15856-+vKDG2PZIwCkiMEd8kjubA^-^server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1__pochta.ru>
Date: Thu, 10 Jun 2010 13:39:52 -0400


Sent to CCL by: "Ol  Ga" [eurisco1-x-pochta.ru]
Dear Upakarasamy Lourderaj,

You can study periodic adsorption - optimize structures and find TS with QST2 (QST3) methods.
Also You can study adsorption on a cluster (a molecular approach), I.e. without PBC conditions.
An example for PBC calculations (one from gaussian example files) :
#p lsda/sto-3g force geom=modred pbc=gammaonly

2d PBC, also test for addredundant with PBC C(H)NC(CN)C(H) - chain (C-N-C-N- core)

0,1
 B   0.7260460000  -0.6287740000   0.0000000000
 N  -0.7260460000  -0.6287740000   0.0000000000
 N   1.4520920000   0.6287740000   0.0000000000
 B  -1.4520920000   0.6287740000   0.0000000000
 B   0.7260460000   1.8863230000   0.0000000000
 N  -0.7260460000   1.8863230000   0.0000000000
 N   1.4520920000   3.1438710000   0.0000000000
 B  -1.4520920000   3.1438710000   0.0000000000
Tv   4.3562760000   0.0000000000   0.0000000000
Tv   0.0000000000   5.0301940000   0.0000000000

11 1 21 F
* * * F
* * * * F

If you are planning to study adsorption on a metallic surface, I think it will be really difficult with Gaussian.

Sincerely,
Ol Ga 

PS: Possible you will need to play with IOPs to reduce time of calculations.

--------------------------------------------------
> From: "Upakarasamy Lourderaj u.lourderaj^-^gmail.com" <owner-chemistry||ccl.net>
Sent: Thursday, June 10, 2010 4:01 PM
To: "Ga, Ol " <eurisco1||pochta.ru>
Subject: CCL:G: PBC with gaussian

> 
> 
> Sent to CCL by: "Upakarasamy  Lourderaj" [u.lourderaj!^!gmail.com]
> I am studying interaction of organic molecules on surfaces.  I would appreciate very much if you let me guide through as to how to give input for such calculations. I want to use periodic boundary condition(PBC) for the surface only, while the organic molecule should treated as a single molecule.  Can we do such calculations using g03?
> 
>


From owner-chemistry@ccl.net Thu Jun 10 15:34:00 2010
From: "David Hose anthrax_brothers{:}hotmail.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: Many cis-trans possible configurations
Message-Id: <-42092-100610143910-19296-+6dIZnIywd82lAI0YKX35A-#-server.ccl.net>
X-Original-From: "David  Hose" <anthrax_brothers=hotmail.com>
Date: Thu, 10 Jun 2010 14:39:09 -0400


Sent to CCL by: "David  Hose" [anthrax_brothers/a\hotmail.com]
John,

You might want to check this pre-published article in J. Phys. Chem. A.

Conformational Sampling of Macrocyclic Alkenes Using a KennardStone-Based Algorithm by 
Veronique Van Speybroeck and coworkers.

http://pubs.acs.org/doi/abs/10.1021/jp1022778

Regards,

Dave.


----------------

Sent to CCL by: John McKelvey [jmmckel**gmail.com]
Hello,

For molecules with several, say 3 or 4, floppy conjugated bonds is
there any code that will sample all possible cis-trans configurations
and report the lowest energy one?

Thanks,

John

-- 
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel^_^gmail.com


From owner-chemistry@ccl.net Thu Jun 10 16:49:00 2010
From: "Antonio Hernandez pescaomayor**gmail.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: IBM's Chemical Kinetics Simulation
Message-Id: <-42093-100609183524-4985-td4/YbMf2/5NDjTMCsIafg%%server.ccl.net>
X-Original-From: Antonio Hernandez <pescaomayor||gmail.com>
Content-Type: multipart/alternative; boundary=00032555517aa2fd0e0488a01601
Date: Wed, 9 Jun 2010 17:34:22 -0430
MIME-Version: 1.0


Sent to CCL by: Antonio Hernandez [pescaomayor-$-gmail.com]

--00032555517aa2fd0e0488a01601
Content-Type: text/plain; charset=ISO-8859-1

The CKS programs works well on Windows XP. On its home page you can download
it from the link download Chemical Kinetics Simulator for Windows 3.1 to
Windows XP<http://www.almaden.ibm.com/st/computational_science/ck/?cks-winfiles>
.
Greetings, Tony.

On Wed, Jun 9, 2010 at 11:15 AM, Geoffrey Hutchison geoffh###pitt.edu <
owner-chemistry^-^ccl.net> wrote:

>
> Sent to CCL by: Geoffrey Hutchison [geoffh*|*pitt.edu]
> Many years ago, IBM had this nice, student-friendly chemical kinetics
> simulation code for "Classic Mac," and Windows 3.1 / Win95. You could input
> reaction mechanisms and rate constants, follow the concentrations as a
> function of time, etc.
> http://www.almaden.ibm.com/st/computational_science/ck/?cks
>
> Now I can't get it to run on modern Macs, and I've had trouble running it
> on Windows too. It's the kind of thing that I can imagine as a great web
> service (not that I'm volunteering!). Does anyone have suggestions for an
> undergrad chemical kinetics tool?
>
> Thanks very much,
> -Geoff
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geoffh!^!pitt.edu
> web: http://hutchison.chem.pitt.edu/
>
>
>
> - This is automatically added to each message by the mailing script ->
>
>

--00032555517aa2fd0e0488a01601
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

The CKS programs works well on Windows XP. On its home page you can downloa=
d it from the link=A0<span class=3D"Apple-style-span" style=3D"font-family:=
 verdana, arial, sans-serif; font-size: 11px; "><a href=3D"http://www.almad=
en.ibm.com/st/computational_science/ck/?cks-winfiles" style=3D"color: rgb(9=
2, 129, 167); ">download Chemical Kinetics Simulator for Windows 3.1 to Win=
dows XP</a>.</span><div>
<font class=3D"Apple-style-span" face=3D"verdana, arial, sans-serif" size=
=3D"3"><span class=3D"Apple-style-span" style=3D"font-size: 11px;">Greeting=
s, Tony.<br></span></font><br><div class=3D"gmail_quote">On Wed, Jun 9, 201=
0 at 11:15 AM, Geoffrey Hutchison geoffh###<a href=3D"http://pitt.edu">pitt=
.edu</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry^-^ccl.net">o=
wner-chemistry^-^ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><br>
Sent to CCL by: Geoffrey Hutchison [geoffh*|*<a href=3D"http://pitt.edu" ta=
rget=3D"_blank">pitt.edu</a>]<br>
Many years ago, IBM had this nice, student-friendly chemical kinetics simul=
ation code for &quot;Classic Mac,&quot; and Windows 3.1 / Win95. You could =
input reaction mechanisms and rate constants, follow the concentrations as =
a function of time, etc.<br>

<a href=3D"http://www.almaden.ibm.com/st/computational_science/ck/?cks" tar=
get=3D"_blank">http://www.almaden.ibm.com/st/computational_science/ck/?cks<=
/a><br>
<br>
Now I can&#39;t get it to run on modern Macs, and I&#39;ve had trouble runn=
ing it on Windows too. It&#39;s the kind of thing that I can imagine as a g=
reat web service (not that I&#39;m volunteering!). Does anyone have suggest=
ions for an undergrad chemical kinetics tool?<br>

<br>
Thanks very much,<br>
-Geoff<br>
<br>
---<br>
Prof. Geoffrey Hutchison<br>
Department of Chemistry<br>
University of Pittsburgh<br>
tel: (412) 648-0492<br>
email: geoffh!^!<a href=3D"http://pitt.edu" target=3D"_blank">pitt.edu</a><=
br>
web: <a href=3D"http://hutchison.chem.pitt.edu/" target=3D"_blank">http://h=
utchison.chem.pitt.edu/</a><br>
<br>
<br>
<br>
- This is automatically added to each message by the mailing script -<br<br=<br<br>
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<br<br>
 =A0 =A0 =A0<a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank">h=
ttp://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br></div>

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From owner-chemistry@ccl.net Thu Jun 10 19:28:00 2010
From: "Gerard Pujadas gerard.pujadas^_^gmail.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: How to perform an "Exact structure search" into eMolecules (or similar database) by using a large list of SMILES
Message-Id: <-42094-100610191756-21932-98BATifLAWO6+3brC2uz7g*_*server.ccl.net>
X-Original-From: Gerard Pujadas <gerard.pujadas:+:gmail.com>
Content-Type: multipart/alternative; boundary=0015174c1030f2bdd70488b53aaa
Date: Fri, 11 Jun 2010 01:17:45 +0200
MIME-Version: 1.0


Sent to CCL by: Gerard Pujadas [gerard.pujadas|a|gmail.com]
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Content-Type: text/plain; charset=ISO-8859-1

Gerard,

My former coworker and colleague Tom Stockfisch forwarded your question from
the CCL mailing list.  Would you mind posting this reply back to the CCL
list for me in case anyone else is interested?

 I have found that eMolecules
> (http://www.emolecules.com/) could provided me with that information
> but the problem is that the "Exact structure search" option seems to
> be available only when you draw the structure in their structure
> editor and not when you use the smiles as a search criteria ...
>

Here is an example URL that does an exact-structure search for "S=C=NC":

 http://www.emolecules.com/cgi-bin/search?t=ex&q=S%3DC%3DNC

The "t=ex" tells the search engine to do an exact search instead of a
substructure search.  "t=ss" (substructure search) is the default if "t"
isn't specified.

Note that you have to use URL encoding on the SMILES, as in the example
above where the '=' sign is encoded as "%3D".

The "exact search" may actually return more than one result. For example, an
exact search for benzene

 http://www.emolecules.com/cgi-bin/search?t=ex&q=c1ccccc1

returns 9 results which includes salt forms as well as deuterated and
13C/14C forms.  In addition, as a "fallback", if the exact structure you
requested isn't found, it will sometimes return a stereoisomer.

Users who use scripts to access eMolecules should also read our Terms of
Service:

 http://www.emolecules.com/doc/terms-of-service.php

Note in particular, "If you use an automated system to access eMolecules,
such as a script or program, then in any 24-hour period you are limited to
at most 1000 distinct queries, and you are limited to a total of 1000 result
per distinct query and 100,000 results per 24-hour period."

Best regards,

Craig James
Chief Technology Officer, eMolecules Inc.

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Content-Transfer-Encoding: quoted-printable

Gerard,<br>
<br>
My former coworker and colleague Tom Stockfisch forwarded your question=20
> from the CCL mailing list. =A0Would you mind posting this reply back to=20
the CCL list for me in case anyone else is interested?<br>
<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I have found that eMolecules<br>
(<a href=3D"http://www.emolecules.com/" target=3D"_blank">http://www.emolec=
ules.com/</a>)
 could provided me with that information<br>
but the problem is that the &quot;Exact structure search&quot; option seems=
 to<br>
be available only when you draw the structure in their structure<br>
editor and not when you use the smiles as a search criteria ...<br>
</blockquote>
<br>
Here is an example URL that does an exact-structure search for &quot;S=3DC=
=3DNC&quot;:<br>
<br>
 =A0<a href=3D"http://www.emolecules.com/cgi-bin/search?t=3Dex&amp;q=3DS%3D=
C%3DNC" target=3D"_blank">http://www.emolecules.com/cgi-bin/search?t=3Dex&a=
mp;q=3DS%3DC%3DNC</a><br>
<br>
The &quot;t=3Dex&quot; tells the search engine to do an exact search instea=
d of a=20
substructure search. =A0&quot;t=3Dss&quot; (substructure search) is the def=
ault if &quot;t&quot;
 isn&#39;t specified.<br>
<br>
Note that you have to use URL encoding on the SMILES, as in the example=20
above where the &#39;=3D&#39; sign is encoded as &quot;%3D&quot;.<br>
<br>
The &quot;exact search&quot; may actually return more than one result. For=
=20
example, an exact search for benzene<br>
<br>
 =A0<a href=3D"http://www.emolecules.com/cgi-bin/search?t=3Dex&amp;q=3Dc1cc=
ccc1" target=3D"_blank">http://www.emolecules.com/cgi-bin/search?t=3Dex&amp=
;q=3Dc1ccccc1</a><br>
<br>
returns 9 results which includes salt forms as well as deuterated and=20
13C/14C forms. =A0In addition, as a &quot;fallback&quot;, if the exact stru=
cture you
 requested isn&#39;t found, it will sometimes return a stereoisomer.<br>
<br>
Users who use scripts to access eMolecules should also read our Terms of
 Service:<br>
<br>
 =A0<a href=3D"http://www.emolecules.com/doc/terms-of-service.php" target=
=3D"_blank">http://www.emolecules.com/doc/terms-of-service.php</a><br>
<br>
Note in particular, &quot;If you use an automated system to access=20
eMolecules, such as a script or program, then in any 24-hour period you=20
are limited to at most 1000 distinct queries, and you are limited to a=20
total of 1000 result per distinct query and 100,000 results per 24-hour=20
period.&quot;<br>
<br>
Best regards,<br><font color=3D"#888888">
<br>
Craig James<br>
Chief Technology Officer, eMolecules Inc.</font>

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