From owner-chemistry@ccl.net Mon May 28 01:21:00 2012 From: "meishway linkon meishway985(~)yahoo.com" To: CCL Subject: CCL: reorganization energy Message-Id: <-47001-120528011605-6406-WU7lPJ0vdk0WrVVZbBebtg],[server.ccl.net> X-Original-From: "meishway linkon" Date: Mon, 28 May 2012 01:16:03 -0400 Sent to CCL by: "meishway linkon" [meishway985{:}yahoo.com] hello everybody! I have compound (pre calculated for optimization and frequency calculations)for which i want to calculate its electron and hole reorganization energy using equation no.2 and 3 on page #5186 in the following paper " Tang, S. and J. Zhang, Rational Design of Organic Asymmetric Donors D1AD2 Possessing Broad Absorption Regions and Suitable Frontier Molecular Orbitals to Match Typical Acceptors toward Solar Cells. The Journal of Physical Chemistry A, 2011. 115(20): p. 5184-5191. " please can any one explain me this equation in detail , and guide me about the method or steps to calculate reorganization energy , I have done but my result are equal to zero. please please guide me in detail about it , I am too confused. From owner-chemistry@ccl.net Mon May 28 17:17:01 2012 From: "Wolf Ihlenfeldt wdi^_^xemistry.com" To: CCL Subject: CCL: PubChem Online Compound Search and Download Message-Id: <-47002-120528151628-1146-sZA9CGr0i/eZGDXbq4fHYA**server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=bcaec51a7c08745b8604c11d8d20 Date: Mon, 28 May 2012 21:16:17 +0200 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi#xemistry.com] --bcaec51a7c08745b8604c11d8d20 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Nancy, this kind of query can (in principle, see below) be easily scripted with the Cactvs Chemoinformatics Toolkit (www.xemistry.com/academic for free academic versions). Here is a tiny sample script which includes a substructure that needs to be matched (here specified as SMARTS: c1nncnn1), combined with exclusion substructures (here: carboxyl, amino, aldehyde), a formula pattern (no halogens), and a property match (zero total charge). The output is a multi-record SD file which includes the PubChem CID as data field. Of course this query and output could and should be further customized. ---snip--- # open PubChem database as a virtual file set fhpub [molfile open ] # open output file, make sure we include the PubChem CID as data field set fhout [molfile open mypubchemcompounds.sdf w writelist E_CID] # perform structure query on PubChem, directly saving results to output fil= e molfile scan $fhpub {and {structure >=3D c1nncnn1} \ {not {structure >=3D C(=3DO)[OH]}} \ {not {structure >=3D [NH2]}} \ {not {structure >=3D [CH](=3DO)}} \ {formula >=3D F0Cl0Br0I0} \ {E_CHARGE =3D 0}} "filelist $fhout" {maxhits 100} molfile close all ----snip --- That query is automatically executed to the extent possible on the PubChem PUG and Entrez servers at NCBI, so you are not downloading every compound for local checking. The problem: Right now I could not get this to complete - I end up with an NCBI Entrez EHistory server error for one of the subqueries. My guess is that there are temporary server problems at NCBI - I have reported the problem. Please feel free to contact me to get this to work in the next days. On Sat, May 26, 2012 at 12:52 AM, Nancy nancy5villaa/gmail.com < owner-chemistry||ccl.net> wrote: > Hi All, > > I have been using the PubChem database to search for uncharged small > molecules. However, even after specifying zero charge, PubChem still > outputs compounds containing amino groups (-NH2) and carboxylic acids > (-COOH); since I am interested in physiological pH, these compounds would > actually be charged. > > Is there some way to exclude molecules containing these functional > groups? I've noticed that there is an option on PubChem to include only > certain atoms, but the search times out at 2 minutes if I try this. I'd > like to exclude halogens and aldehydes as well, can this be specified? > Finally, after searching for numerous compounds, how could all of them be > downloaded into an organized compound library? > > If there is another online compound database besides PubChem that can be > easily searched and has the same or better functionality, I'd greatly > appreciate any info about it. > > Thanks, > Nancy > > > > --=20 Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi||xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W.= D. Ihlenfeldt Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 --bcaec51a7c08745b8604c11d8d20 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Nancy,

this kind of query can (in principle, see below) be ea= sily scripted with the Cactvs Chemoinformatics Toolkit (www.xemistry.com/academic for free academic v= ersions).

Here is a tiny sample script which
includes a substructure that need= s to be matched (here specified as SMARTS: c1nncnn1),
=C2=A0combined wit= h exclusion substructures (here: carboxyl, amino, aldehyde), a formula patt= ern (no halogens), and a property match (zero total charge). The output is = a multi-record SD file which includes the PubChem CID as data field.

Of course this query and output could and should be further customized.=

---snip---
# open PubChem database as a virtual file
set fhpu= b [molfile open <pubchem>]
# open output file, make sure we includ= e the PubChem CID as data field
set fhout [molfile open mypubchemcompounds.sdf w writelist E_CID]
# perf= orm structure query on PubChem, directly saving results to output file
m= olfile scan $fhpub {and {structure >=3D c1nncnn1} \
=C2=A0=C2=A0=C2= =A0 {not {structure >=3D C(=3DO)[OH]}} \
=C2=A0=C2=A0=C2=A0 {not {structure >=3D [NH2]}} \
=C2=A0=C2=A0=C2=A0 = {not {structure >=3D [CH](=3DO)}} \
=C2=A0=C2=A0=C2=A0 {formula >= =3D F0Cl0Br0I0} \=C2=A0
=C2=A0=C2=A0=C2=A0 {E_CHARGE =3D 0}} "file= list $fhout" {maxhits 100}=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0
molfile c= lose all
----snip ---

That query is automatically executed to the extent possible on the PubC= hem PUG and Entrez servers at NCBI, so you are not downloading every compou= nd for local checking.

The problem: Right now I could not get this t= o complete - I end up with an NCBI Entrez EHistory server error for one of = the subqueries. My guess is that there are temporary server problems at NCB= I - I have reported the problem.

Please feel free to contact me to get this to work in the next days.

On Sat, May 26, 2012 at 12:52 AM, Nancy= nancy5villaa/gmail.com = <owner-chem= istry||ccl.net> wrote:
Hi All,

I have been using the PubChem= database to search for uncharged small molecules.=C2=A0 However, even afte= r specifying zero charge, PubChem still outputs compounds containing amino = groups (-NH2) and carboxylic acids (-COOH); since I am interested in physio= logical pH, these compounds would actually be charged.

Is there some way to exclude molecules containing these functional grou= ps?=C2=A0 I've noticed that there is an option on PubChem to include on= ly certain atoms, but the search times out at 2 minutes if I try this.=C2= =A0 I'd like to exclude halogens and aldehydes as well, can this be spe= cified?=C2=A0 Finally, after searching for numerous compounds, how could al= l of them be downloaded into an organized compound library?

If there is another online compound database besides PubChem that can b= e easily searched and has the same or better functionality, I'd greatly= appreciate any info about it.

Thanks,
Nancy






--
Wolf-D. Ihlenfeldt -=C2= =A0 Xemistry GmbH - w= di||xemistry.com
Phone: +49 6174 201455 - Fax +49 6174 209665
---<= br>xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr.= W. D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
HR K=C3=B6nigs= tein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719

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