From owner-chemistry@ccl.net Wed Aug 10 09:11:02 2011 From: "Vera Cathrine vera.cathrine-$-yahoo.com" To: CCL Subject: CCL:G: G03: CASSCF Message-Id: <-45236-110810044156-29774-nsjecATegD9ZCJtvGQ7snA[]server.ccl.net> X-Original-From: "Vera Cathrine" Date: Wed, 10 Aug 2011 04:41:52 -0400 Sent to CCL by: "Vera Cathrine" [vera.cathrine!^!yahoo.com] Dear All, I am trying to study the cis-trans photoisomerisation of an organic photoreceptor by excited state dynamics inside a protein using CASSCF. The full pi active space in this organic compound is considered as CAS(16,14). Due to computational expenses I like to reduce this to smaller CAS like CAS(8,8) or less for my QM/MM excited state dynamics using surface hoping algorithm. I have used G03 to reduce the active space step by step. I have taken same strategy for both S0 and S1. I chose the swapping the orbitals based on visual inspection (chemical intuition) and following occupation numbers. I exclude the orbitals with closest value to 0 or 2 in every step. Is this a good way to reduce the active space? It has been recommended in the literature that If I want to study the S1 state, I should use state-averaged orbitals for my S1 excited state dynamics to avoid convergence issues. Which orbitals are more proper for this purpose (Natural or canonical)?Why? Any suggestion is greatly appreciated. Kind wishes, Vera Cathrine From owner-chemistry@ccl.net Wed Aug 10 12:06:01 2011 From: "James Thomas Metz James.Metz^_^Abbott.com" To: CCL Subject: CCL: models to predict small molecule fluorescence, publications? Message-Id: <-45237-110810120321-14249-MIm+GacTAQtbcqK5SQJpfQ%x%server.ccl.net> X-Original-From: "James Thomas Metz" Date: Wed, 10 Aug 2011 12:03:17 -0400 Sent to CCL by: "James Thomas Metz" [James.Metz+/-Abbott.com] CCL, Can someone direct me to any publications describing models to predict small molecule fluorescence using cheminformatics-type approaches i.e., pattern recognition of aromatic rings or substructures which have a high probability of fluorescence. I am trying to avoid QM or semi-empirical approaches, if possible. Alternatively, if someone is aware of databases of compounds which have been tested for fluorescence and contain positives and negatives that would be excellent. I have access to software that would allow me to construct in-house models given enough quality data. Thank you. Regards, Jim Metz Abbott Laboratories From owner-chemistry@ccl.net Wed Aug 10 15:16:01 2011 From: "Cristian Bologa cbologa^^salud.unm.edu" To: CCL Subject: CCL: models to predict small molecule fluorescence, publications? Message-Id: <-45238-110810151402-9162-RfXnB0r2drVyhZfpbeaQWA/./server.ccl.net> X-Original-From: "Cristian Bologa" Content-Type: multipart/alternative; boundary="=__PartC0EFC17C.1__=" Date: Wed, 10 Aug 2011 13:13:48 -0600 Mime-Version: 1.0 Sent to CCL by: "Cristian Bologa" [cbologa,salud.unm.edu] This is a MIME message. If you are reading this text, you may want to consider changing to a mail reader or gateway that understands how to properly handle MIME multipart messages. --=__PartC0EFC17C.1__= Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Hi Jim, =20 If HTS quality data is good enough for you, then you should look at some = of the following assays in Pubchem: 587, 588, 589, 590, 591, 592, 593, = 594, 708, 709, 774, 923, 1775, 1776. =20 Good luck, =20 Cristian Bologa, Ph.D. Research Associate Professor, Division of Biocomputing, Univ. of New Mexico, School of Medicine, MSC11 6145, Research Incubator Building, 2703 Frontier NE, Albuquerque, NM 87131 tel: +1-505-272-6509 fax:+1-505-272-0238 =20 http://scholar.google.com/citations?user=3Dpw5di3IAAAAJ >>> "James Thomas Metz James.Metz^_^Abbott.com" = 8/10/2011 10:03 AM >>> Sent to CCL by: "James Thomas Metz" [James.Metz+/-Abbott.com] CCL, Can someone direct me to any publications describing models to predict = small molecule fluorescence using cheminformatics-type approaches i.e., = pattern recognition of aromatic rings or substructures which have a high = probability of fluorescence. I am trying to avoid QM or semi-empirical approaches, if possible. Alternatively, if someone is aware of databases of compounds which have = been tested for fluorescence and contain positives and negatives that would be = excellent. I have access to software that would allow me to construct = in-house models given enough quality data. Thank you. Regards, Jim Metz Abbott Laboratories -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=__PartC0EFC17C.1__= Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Content-Description: HTML
Hi Jim,
 
If HTS quality data is good enough for you, then you should look at = some of the following assays in Pubchem: 587, 588, 589, 590, 591, 592, = 593, 594, 708, 709, 774, 923, 1775, 1776.
 
Good luck,
 
Cristian Bologa, Ph.D.
Research = Associate Professor,
Division of Biocomputing,
Univ. = of New Mexico, School of Medicine,
<= FONT size=3D2>
MSC11 6145, Research Incubator Building,
2703 Frontier NE, = Albuquerque, NM 87131
tel: +1-505-272-6509
fax:+1-505-272-0238
 

>>> "James Thomas Metz James.Metz^_^Abbott.com" = <owner-chemistry#%#ccl.net> 8/10/2011 10:03 AM >>>

Sent= to CCL by: "James Thomas Metz" [James.Metz+/-Abbott.com]
CCL,

Ca= n someone direct me to any publications describing models to predict small = molecule fluorescence using cheminformatics-type approaches i.e., pattern = recognition of aromatic rings or substructures which have a high probabilit= y
of fluorescence.

I am trying to avoid QM or semi-empirical = approaches, if possible.

Alternatively, if someone is aware of = databases of compounds which have been
tested for fluorescence and = contain positives and negatives that would be excellent.  I have = access to software that would allow me to construct in-house
models = given enough quality data.

Thank you.

Regards,
Jim = Metz
Abbott Laboratories



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