From owner-chemistry@ccl.net Thu Feb 5 03:41:00 2009 From: "Cristian V. Diaconu cvdiaconu#,#rice.edu" To: CCL Subject: CCL:G: Broken Symmetry Singlet Excited State Message-Id: <-38556-090205033719-3453-OPYBOhNxxiooABKVUCTQww()server.ccl.net> X-Original-From: "Cristian V. Diaconu" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 05 Feb 2009 02:37:05 -0600 MIME-Version: 1.0 Sent to CCL by: "Cristian V. Diaconu" [cvdiaconu{=}rice.edu] The value of S^2 you have to use is the one *before* projection (in the example you gave me 0.8631) After projection S^2 should be 0 for a singlet. In your example S^2 after "Annihilation of the first spin contaminant", in this case triplet, is 0.4136, and comes from higher spin components. This, unfortunately, means the formula you are using does not hold. In the case of broken symmetry calculation for H2, the broken symmetry determinant is a mixture of pure singlet determinant and pure triplet determinant with S_z=0. The mixing ratio is related to your fSC. For H2 at infinite separation, the broken symmetry determinant is an equal mixture of singlet and triplet (S_z=0). This limiting case is the only case that DFT handles well. If your is not close to 1, then the projection using this approach is not very good. See the following example for H2 at d(H-H) = 9.5 a0 (almost dissociated), and d(H-H) = 4.2 a0 (right around where the broken symmetry solution becomes more stable). Chris Here's an example for H2 UB3LYP/6-311++G** guess=mix d(H-H) = 9.5 a0: SCF Done: E(UB+HF-LYP) = -1.00452667499 A.U. after 5 cycles Convg = 0.5289D-08 -V/T = 2.0119 S**2 = 1.0000 KE= 9.927556920227D-01 PE=-2.202132474486D+00 EE= 9.958694958153D-02 Annihilation of the first spin contaminant: S**2 before annihilation 1.0000, after 0.0000 d(H-H) = 4.2 a0: SCF Done: E(UB+HF-LYP) = -1.01321186020 A.U. after 8 cycles Convg = 0.3446D-08 -V/T = 2.0689 S**2 = 0.8435 KE= 9.479387091822D-01 PE=-2.439555548275D+00 EE= 2.403097407996D-01 Annihilation of the first spin contaminant: S**2 before annihilation 0.8435, after 0.0000 Sue Lam chsue2004#,#yahoo.com wrote: > Hello Chris, > > > > Thank you very much for your reply. I am studying a reaction, in which > the transition state contain biradical character. I have tired to > extract the energy of the pure singlet from the broken symmetry state by > using the spin-correction procedure which was proposed by Yamaguchi et > al (/Chem. Phys. Lett. /*1994*, /231/, 25–33)// > > > > E(singlet) = E(broken symmetry from UDFT) + fSC[E(broken symmetry from > UDFT – E(triplet from UDFT)) > > > > Where fSC = 1 / [3 - 1] > > > > S^2: expectation value of the total spin > > > > The S^2 before and after the annihilation are listed in the Gaussian > output. In my case, > > > > Annihilation of the first spin contaminant: > > S^2 before annihilation 0.8631, after 0.4136 > > > > I am not sure that whether I should use the S^2 before or after the > annihilation for the projection method. > > > > Best regards, > > Sue > > --- On *Wed, 2/4/09, Cristian V. Diaconu cvdiaconu!A!rice.edu > //* wrote: > > From: Cristian V. Diaconu cvdiaconu!A!rice.edu > > Subject: CCL:G: Broken Symmetry Singlet Excited State > To: "L, Sue " > Date: Wednesday, February 4, 2009, 2:15 PM > > Sent to CCL by: "Cristian V. Diaconu" [cvdiaconu~!~rice.edu] > Hello Sue, > > The total energy reported by Gaussian is not for 'annihilated' wave > function, but for the single determinant that it uses in the Kohn-Sham scheme > (for DFT there isn't really any wave function). There are ways to extract > the energy of the pure singlet from the broken symmetry state, but for DFT they > only work in certain cases. Please look at discussions in: > > J. Chem. Phys. 121, 10026 (2004) > J. Chem. Phys. 74, 5737 (1981) > Coord. Chem. Rev. 238–239, 187 (2003) > C. J. Cramer, in Essentials of Computational Chemistry. Theories and Models. > (Wiley, Chichester, 2002), Chap. 14.4, pp. 456 – 459. > > For example, for a molecule with two unpaired electrons on two sites which > interact weakly (e.g., H2 molecule stretched, with a large bond length, say 10 > Angstroms), if ~ 1, > > E(singlet) = 2 E(broken sym) - E(triplet) > > I hope this helps. If you have further questions, please include a little > detail on the system you are looking at. > > Best regards, > Chris > > Sue L chsue2004(~)yahoo.com wrote: > > Sent to CCL by: "Sue L" [chsue2004..yahoo.com] > > Hi, > > I am running a DFT open-shell singlet calculation using Gaussian 03 to > obtain a broken symmetry singlet excited state. Does anyone know whether the > electronic energy calculated at the end based on the annihilated wave function > or not? > > Thank you very much! > > > > Best regards, > > Sue> > > > > > > -- Cristian V. Diaconu > Postdoctoral Research Associate > Department of Chemistry - MS60 > Rice University > PO Box 1892 > Houston, TX 77251-1892 > Phone: 713-348-3734 > Email: cvdiaconu-x-rice.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > From owner-chemistry@ccl.net Thu Feb 5 06:14:01 2009 From: "Serge Dom serge.dom(-)gmail.com" To: CCL Subject: CCL: H3CC react better with triple bonds systems Message-Id: <-38557-090205053839-17509-y+gCr+eSyyz9uA+o1zoVZA-.-server.ccl.net> X-Original-From: Serge Dom Content-Type: multipart/alternative; boundary=0015174c3f4c9c1ed9046229749e Date: Thu, 5 Feb 2009 12:34:56 +0200 MIME-Version: 1.0 Sent to CCL by: Serge Dom [serge.dom|a|gmail.com] --0015174c3f4c9c1ed9046229749e Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello, I would like to ask if anybody knows quantum chemical explanations why methylcarbyne molecule (H3C-C) react much better with the system with CC triple bonds instead of the systems with CC double bonds? Methylcarbyne molecule is in doublet or in quartet states. Thank you Serge --0015174c3f4c9c1ed9046229749e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello,
 
I would like to ask if anybody knows q= uantum chemical explanations why methylcarbyne molecule (H3C-C) react much = better  with the system with CC triple bonds instead of the systems wi= th CC double bonds? Methylcarbyne molecule is in doublet or in quartet stat= es.
 
Thank you  Serge
--0015174c3f4c9c1ed9046229749e-- From owner-chemistry@ccl.net Thu Feb 5 08:42:00 2009 From: "=?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= jgcj%a%fct.unl.pt" To: CCL Subject: CCL: Target identification for reported inhibitor Message-Id: <-38558-090205051123-15504-0D3mwmnFJdmfLiQv9SJ1uw%%server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= Content-Type: multipart/alternative; boundary=0016e6d27c9088e9d70462291f97 Date: Thu, 5 Feb 2009 10:11:09 +0000 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= [jgcj#,#fct.unl.pt] --0016e6d27c9088e9d70462291f97 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable if you want just A target, you could run some blind docking experiments... though, as good as it gets, you'de be getting merely predictions... G. --=20 Gon=E7alo Justino, Ph.D. ---------------------------------------------------- [Computational & Radical BioChemistry] Requimte/CQFB - Department of Chemistry Faculty of Sciences and Technology New University of Lisbon 2829-516 Caparica Portugal Phone: (+351) 212 948 300 ext. 10971 Fax: (+351) 212 948 550 ---------------------------------------------------- All saints have a past, all sinners have a future. 2009/2/3 David A. Mannock dmannock++ualberta.ca > A target or the target? Sounds like you need a biochemist and the > willingness to do some *experiments*! Please excuse the use of the dirty > word here! David > > > > At 04:26 AM 03/02/2009, you wrote: > > Hi All; > I have a molecule in my hand which is well reported antitubercular drug b= ut > the respective target protein is not known! Can anyone suggest me how can= i > find the target for this ligand? > > --0016e6d27c9088e9d70462291f97 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable if you want just A target, you could run some blind docking experiments... = though, as good as it gets, you'de be getting merely predictions...
=
G.

--
Gon=E7alo Justino, Ph.D.
------------= ----------------------------------------
[Computational & Radical BioChemistry]
Requimte/CQFB - Department of= Chemistry
Faculty of Sciences and Technology
New University of Lisbo= n
2829-516 Caparica
Portugal
Phone: (+351) 212 948 300 ext. 10971<= br> Fax: (+351) 212 948 550
------------------------------------------------= ----
All saints have a past, all sinners have a future.


2009/2/3 David A. Mannock dmannock++ualberta.ca <owner-chemistry+/-ccl.net>
=
A target or the target? Sounds like you need a biochemist and the willingness to do some experiments! Please excuse the use of the dirty word here! David



At 04:26 AM 03/02/2009, you wrote:
Hi All;
I have a molecule in my hand which is well reported antitubercular drug but the respective target protein is not known! Can anyone suggest me how can i find the target for this ligand?


--0016e6d27c9088e9d70462291f97-- From owner-chemistry@ccl.net Thu Feb 5 09:16:01 2009 From: "Barry Hardy barry.hardy:-:vtxmail.ch" To: CCL Subject: CCL: Predictive ADME and Toxicology Workshop, Oxford July 2009, Bursary awards available Message-Id: <-38559-090205085700-29702-MKOnjLcvikrgO1t75/TkYQ~!~server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 05 Feb 2009 14:56:29 +0100 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy,vtxmail.ch] We are running a Predictive ADME and Toxicology workshop week at Oxford University 27 - 31 July 2009. We will take a hands-on case study approach using a variety of methods applied to ADME and Tox datasets and endpoints. More information on program can be found at: Blog: http://barryhardy.blogs.com/cheminfostream/ Pdf: http://barryhardy.blogs.com/files/echeminfoadmetprogramoxford09-1.pdf Web: http://echeminfo.com/COMTY_oxfordadmet09 A Bursary Award will be used to support the attendance of a selection of academic participants, who may be working in any area of research related to predictive ADME and toxicology. To apply for the bursary please send an email with a) description of your research (ca. 500 words); b) your training needs (ca. 500 words), c) your CV to echeminfo -[at]- douglasconnect.com by 20 February 2009. best regards Barry Hardy eCheminfo Community of Practice Douglas Connect GmbH Switzerland barry.hardy -[at]- douglasconnect.com Tel: +41 61 851 0170 From owner-chemistry@ccl.net Thu Feb 5 09:53:01 2009 From: "Jean-Christophe Poully poully%x%galilee.univ-paris13.fr" To: CCL Subject: CCL: how to deal with the result of the ONIOM method Message-Id: <-38560-090205084041-22372-2oUbksw4S4pITttNE5IrdQ|,|server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Thu, 05 Feb 2009 14:40:24 +0100 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully*_*galilee.univ-paris13.fr] If I understood correctly, you want to scan the=20 potential energy surface while docking your=20 ligand, is it right? I'm afraid not to be able to=20 help you for that, I have never done such a study... Sorry! Good luck for your work, Jean-Christophe At 02:52 05/02/2009, you wrote: >Sent to CCL by: "Zhong jie Liang" [zjliang#,#mail.shcnc.ac.cn] > Thanks for Jean-Christophe and Isabelle's=20 > help. I have known my charge problem and solved it. > Now I am doing the first optimization. The=20 > next is to do the scan.I don't know how to deal=20 > with the result completely. What I need to do=20 > is to get the energy of every step and then=20 > make an adiabatic potential energy surface as a=20 > function of two different distances. Is that right? > Hope to get answer very much. Thanks. > > > > > > > > ZhongjieLiang > zjliang,+,mail.shcnc.ac.cn > Shanghai Institute of Materia Medica > > > >-=3D This is automatically added to each message by the mailing script =3D-Jean-Christophe Poully Doctorant dans l'=E9quipe AMIBES Laboratoire de Physique des Lasers Institut Galil=E9e 99, avenue JB Cl=E9ment 93430 VILLETANEUSE Bureau B002 0149403853=20 From owner-chemistry@ccl.net Thu Feb 5 11:07:00 2009 From: "Carlos Lagos A. carlos,cbuc.cl" To: CCL Subject: CCL: Target identification for reported inhibitor Message-Id: <-38561-090205110330-13350-4X4PxMtV4LHfK0NH/45eaA-.-server.ccl.net> X-Original-From: "Carlos Lagos A." Content-Type: multipart/alternative; boundary="----=_NextPart_000_001D_01C9878D.4AE9E1F0" Date: Thu, 5 Feb 2009 12:28:47 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos Lagos A." [carlos|cbuc.cl] This is a multi-part message in MIME format. ------=_NextPart_000_001D_01C9878D.4AE9E1F0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I guess some alternative if you have only the ligand and only in silico experiment will be conducted: First get all the information about = potential mechanism of action or experiments already done, then try similarity searches (against PDB ligands database for instance, Ligand.info, = Pubchem, etc), hits can give you some ideas regarding the potential mechanism of action of the ligand you have. Then go for all solved structures for MT = in the PDB, and watch the co-crystallized ligands in the Ligand Hits tab, = see if there=B4s some structural similarity. I don=B4t know but there must = be a way to download all the PDB entries and then select only the ligands, ie, = build your own MT PDB-based ligand database, then you could try a similarity search over that structures. If all fail, you can build a non-redundant database of MT targets, clean it and prepared for blind docking with = your ligands. Good luck :-) =20 QF Carlos Lagos A.=20 Centre for Bioinformatics, Faculty of Biological Sciences Medicinal Chemistry Laboratory, Faculty of Chemistry P. Universidad Catolica de Chile I Portugal # 49, Zocalo ZIP 8330025 I Santiago =96 Chile Phone: + 56 2 6862269 I http://www.cbuc.cl=20 _____ =20 De: owner-chemistry+carlos=3D=3Dcbuc.cl]_[ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl]_[ccl.net] En nombre de = Gon=E7alo C. Justino jgcj%a%fct.unl.pt Enviado el: Jueves, 05 de Febrero de 2009 6:11 Para: Lagos, Carlos F Asunto: CCL: Target identification for reported inhibitor =20 if you want just A target, you could run some blind docking = experiments... though, as good as it gets, you'de be getting merely predictions... G. --=20 Gon=E7alo Justino, Ph.D. ---------------------------------------------------- [Computational & Radical BioChemistry] Requimte/CQFB - Department of Chemistry Faculty of Sciences and Technology New University of Lisbon 2829-516 Caparica Portugal Phone: (+351) 212 948 300 ext. 10971 Fax: (+351) 212 948 550 ---------------------------------------------------- All saints have a past, all sinners have a future. 2009/2/3 David A. Mannock dmannock++ualberta.ca = > A target or the target? Sounds like you need a biochemist and the willingness to do some experiments! Please excuse the use of the dirty = word here! David At 04:26 AM 03/02/2009, you wrote: Hi All; I have a molecule in my hand which is well reported antitubercular drug = but the respective target protein is not known! Can anyone suggest me how = can i find the target for this ligand? =20 ------=_NextPart_000_001D_01C9878D.4AE9E1F0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

I guess some = alternative if you have only the ligand and only in silico experiment will be = conducted: =A0First get all the information about potential mechanism of action or = experiments already done, then try similarity searches (against PDB ligands database = for instance, Ligand.info, Pubchem, etc), hits can give you some ideas = regarding the potential mechanism of action of the ligand you have. Then go for = all solved structures for MT in the PDB, and watch the co-crystallized ligands in = the Ligand Hits tab, see if there=B4s some structural similarity. I don=B4t know = but there must be a way to download all the PDB entries and then select only the = ligands, ie, build your own MT PDB-based ligand database, then you could try a = similarity search over that structures. If all fail, you can build a non-redundant database of MT targets, clean it and prepared for blind docking with = your ligands. Good luck J

 =

QF Carlos Lagos A. =
Centre for Bioinformatics, Faculty of Biological Sciences
Medicinal Chemistry Laboratory, Faculty of Chemistry
P. Universidad Catolica de Chile I Portugal # 49, Zocalo
ZIP 8330025 = I Santiago – Chile
Phone: + 56 2 6862269 = I http://www.cbuc.cl<= /font>

De: owner-chemistry+carlos=3D=3Dcbuc.cl]_[ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl]_[ccl.net] En nombre de Gon=E7alo C. Justino jgcj%a%fct.unl.pt
Enviado el: Jueves, = 05 de = Febrero de 2009 6:11
Para: Lagos, Carlos F =
Asunto: CCL: Target = identification for reported inhibitor

 

if you want = just A target, you could run some blind docking experiments... though, as good = as it gets, you'de be getting merely predictions...

G.

--
Gon=E7alo Justino, Ph.D.
----------------------------------------------------
[Computational & Radical BioChemistry]
Requimte/CQFB - Department of Chemistry
Faculty of Sciences and Technology
New University of Lisbon
2829-516 Caparica
Portugal
Phone: (+351) 212 948 = 300 ext. 10971
Fax: (+351) 212 948 = 550
----------------------------------------------------
All saints have a past, all sinners have a future.

 

------=_NextPart_000_001D_01C9878D.4AE9E1F0-- From owner-chemistry@ccl.net Thu Feb 5 11:58:01 2009 From: "Do Quoc-Tuan quoctuan.do**greenpharma.com" To: CCL Subject: CCL: Target identification for reported inhibitor Message-Id: <-38562-090205110642-13651-eJ9s/Mp8/sWLLLm7VN7KNw[a]server.ccl.net> X-Original-From: Do Quoc-Tuan Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 05 Feb 2009 15:59:29 +0100 MIME-Version: 1.0 Sent to CCL by: Do Quoc-Tuan [quoctuan.do---greenpharma.com] Dear Hirdesh, You may look at what we published : Bernard P, Dufresne-Favetta C, Favetta P, Do QT, Himbert F, Zubrzycki S, Scior T, Lugnier C. Application of drug repositioning strategy to TOFISOPAM. Curr Med Chem. 2008;15(30):3196-203. Do QT, Lamy C, Renimel I, Sauvan N, André P, Himbert F, Morin-Allory L, Bernard P. Reverse pharmacognosy: identifying biological properties for plants by means of their molecule constituents: application to meranzin. Planta Med. 2007 Oct;73(12):1235-40. Do QT, Renimel I, Andre P, Lugnier C, Muller CD, Bernard P. Reverse pharmacognosy: application of selnergy, a new tool for lead discovery. The example of epsilon-viniferin. Curr Drug Discov Technol. 2005 Sep;2(3):161-7. Please feel free to contact me should you want to discuss this further (collaborations...) Best regards, Quoc-Tuan hirdesh kumar hirdeshs8]_[gmail.com a écrit : > Hi All; > I have a molecule in my hand which is well reported antitubercular > drug but the respective target protein is not known! Can anyone > suggest me how can i find the target for this ligand? > > -- Quoc-Tuan Do, PhD Chemoinformatics Manager ============================================ Greenpharma S.A. 3, Allée du Titane 45100 Orléans FRANCE Tél : +33.2.38.25.99.80 Fax : +33.2.38.25.99.65 mail: quoctuan.do%greenpharma.com web : http://www.greenpharma.com ============================================ Le contenu de ce message et de toute piece jointe est confidentiel et est adresse exclusivement au(x) destinaire(s). Si vous recevez ce message par erreur, veuillez le detruire et informer immediatement l'expediteur. Greenpharma ne peut etre tenu responsable des erreurs de transmission inherant aux courriels, a l'interception et aux modifications frauduleuses du contenu du message et de ses pieces jointes. Greenpharma a pris les précautions raisonnables contre les logiciels malveillants. Par consequent, Greenpharma decline toute responsabilite quant a un eventuel dommage ou contamination de votre systeme informatique. The content of this message and any attachment is confidential and is exclusively intended to its recipient(s). If you receive this e-mail by error, please delete it and notify its sender immediately. Greenpharma is not liable for any transmission errors due to e-mail, any deceptive interception and modification of the content of this message and of its attachment(s). Greenpharma has taken reasonable measures against malware. Therefore, Greenpharma is not liable for any damage or contamination of your information system. From owner-chemistry@ccl.net Thu Feb 5 21:21:02 2009 From: "Zhong jie Liang zjliang!A!mail.shcnc.ac.cn" To: CCL Subject: CCL: how to deal with the result in the ONIOM method Message-Id: <-38563-090205212017-8964-3FGNnPUlwe5pwOlFssdnsQ*|*server.ccl.net> X-Original-From: "Zhong jie Liang" Date: Thu, 5 Feb 2009 21:20:13 -0500 Sent to CCL by: "Zhong jie Liang" [zjliang#%#mail.shcnc.ac.cn] Thank Jean-Christophe all the same. I am studying on a chemistry mechanism of a reaction to verify if it is an SN1 or SN2 mechanism.I know I should make a potential energy surface when increase the distance of the two atom whose bond is broking and decrease the distanse whose bond is forming. What else should I do to analyse the result completely or what other should I do? The references would be appreciated very much. ZhongjieLiang zjliang##mail.shcnc.ac.cn Shanghai Institute of Materia Medica