From owner-chemistry@ccl.net Wed Jun 20 04:37:00 2012 From: "Eli Lam elizabeth.shlam|*|gmail.com" To: CCL Subject: CCL: Differences between NBO orbitals and molecular orbitals Message-Id: <-47109-120620034823-21452-KaY3O9JjCUb0BClTSpjHFw]^[server.ccl.net> X-Original-From: "Eli Lam" Date: Wed, 20 Jun 2012 03:48:22 -0400 Sent to CCL by: "Eli Lam" [elizabeth.shlam+*+gmail.com] Dear CCLers, I would like to ask why is orbitals plotted using NBO analysis different from the molecular orbitals without using NBO? I have learnt that NBO will lead to a more localized orbital distribution while MO is more delocalized. Yet, I'm confused why the molecular orbitals output from NBO plots are much different > from molecular orbitals: the electron density localized on different atoms when comparing the molecular orbitals from NBO output and the single point run. Please advise! Thank you very much for your help! Best regards, Eli From owner-chemistry@ccl.net Wed Jun 20 10:44:00 2012 From: "Jens Spanget-Larsen spanget%%ruc.dk" To: CCL Subject: CCL:G: how to calculate quantum yield by computational methods Message-Id: <-47110-120620040556-10519-7/BvtmUMduWwQW4IAfxbQg]|[server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Type: multipart/alternative; boundary="------------070807070302060700030408" Date: Wed, 20 Jun 2012 10:05:47 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget-x-ruc.dk] This is a multi-part message in MIME format. --------------070807070302060700030408 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Ram Shankar! Theoretical prediction of quantum yields is an extremely difficult task. The fluorescence quantum yield is a measure of the fraction of the absorbed number of photons that are emitted by direct radiative transfer back to the ground state. Hence, in order to calculate the quantum yield, you need to take account of all other possible routes of energy transfer in the excited state, including a variety of possible photophysical and photochemical pathways (intersystem crossing, quenching due to interaction with other species, etc, etc). This makes theoretical estimates of quantum yields terribly complicated. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget_+_ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ On 6/18/2012 21:15, Ram Shankar S ramchemistry2011===gmail.com wrote: > Sent to CCL by: "Ram Shankar S" [ramchemistry2011]^[gmail.com] > Dear All, > I am doing TDDFT calculation of curtain dyes using Gaussian09 software. I would like to know how to calculate quantum yield. Please help me. > > Thanks in advance > > With Regards > RAAM> > ======= Email scanned by PC Tools - No viruses or spyware found. (Email Guard: 9.0.0.888, Virus/Spyware Database: 6.19950) http://www.pctools.com/ ======= --------------070807070302060700030408 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Ram Shankar!
Theoretical prediction of quantum yields is an extremely difficult task. The fluorescence quantum yield is a measure of the fraction of the absorbed number of photons that are emitted by direct radiative transfer back to the ground state. Hence, in order to calculate the quantum yield, you need to take account of all other possible routes of energy transfer in the excited state, including a variety of possible photophysical and photochemical pathways (
intersystem crossing, quenching due to interaction with other species, etc, etc). This makes theoretical estimates of quantum yields terribly complicated.
Yours, Jens >--<
  ------------------------------------------------------
  JENS SPANGET-LARSEN         Office:      +45 4674 2710
  Dept. of Science (18.1)     Fax:         +45 4674 3011
  Roskilde University         Mobile:      +45 2320 6246
  P.O.Box 260                 E-Mail:     spanget_+_ruc.dk
  DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget
  ------------------------------------------------------

On 6/18/2012 21:15, Ram Shankar S ramchemistry2011===gmail.com wrote:
Sent to CCL by: "Ram Shankar S" [ramchemistry2011]^[gmail.com]
Dear All,
	I am doing TDDFT calculation of curtain dyes using Gaussian09 software. I would like to know how to calculate quantum yield. Please help me.

Thanks in advance

With Regards
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--------------070807070302060700030408-- From owner-chemistry@ccl.net Wed Jun 20 11:19:00 2012 From: "Jim Kress ccl_nospam:-:kressworks.com" To: CCL Subject: CCL: Differences between NBO orbitals and molecular orbitals Message-Id: <-47111-120620084323-5907-dHmwRYXgpnJ+DR9Nhz6A6A=-=server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 20 Jun 2012 08:43:06 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam^-^kressworks.com] Read this: http://www.chem.wisc.edu/~nbo5/ Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com],[ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com],[ccl.net] On Behalf > Of Eli Lam elizabeth.shlam|*|gmail.com > Sent: Wednesday, June 20, 2012 3:48 AM > To: Kress, Jim > Subject: CCL: Differences between NBO orbitals and molecular orbitals > > > Sent to CCL by: "Eli Lam" [elizabeth.shlam+*+gmail.com] Dear CCLers, > > I would like to ask why is orbitals plotted using NBO analysis different > from > the molecular orbitals without using NBO? I have learnt that NBO will lead to > a more localized orbital distribution while MO is more delocalized. Yet, I'm > confused why the molecular orbitals output from NBO plots are much > different > > from molecular orbitals: the electron density localized on different > > atoms when > comparing the molecular orbitals from NBO output and the single point run. > Please advise! > > Thank you very much for your help! > Best regards, > EliTo > recover the email address of the author of the message, please change the > strange characters on the top line to the ],[ sign. You can also look up the X- > Original-From: line in the mail header.> From owner-chemistry@ccl.net Wed Jun 20 11:53:00 2012 From: "Jim Kress ccl_nospam###kressworks.com" To: CCL Subject: CCL:G: how to calculate quantum yield by computational methods Message-Id: <-47112-120620112418-25081-QOVQhdPDDUtAYXk1KfXKuA%server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_001D_01CD4ED7.35100570" Date: Wed, 20 Jun 2012 11:24:07 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam#%#kressworks.com] This is a multipart message in MIME format. ------=_NextPart_000_001D_01CD4ED7.35100570 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit > This makes theoretical estimates of quantum yields terribly complicated. Yes, but is it not doable? Are there any examples where people have attempted to do theoretical prediction of quantum yields? Jim > From: owner-chemistry+ccl_nospam==kressworks.com{=}ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com{=}ccl.net] On Behalf Of Jens Spanget-Larsen spanget%%ruc.dk Sent: Wednesday, June 20, 2012 4:06 AM To: Kress, Jim Subject: CCL:G: how to calculate quantum yield by computational methods Dear Ram Shankar! Theoretical prediction of quantum yields is an extremely difficult task. The fluorescence quantum yield is a measure of the fraction of the absorbed number of photons that are emitted by direct radiative transfer back to the ground state. Hence, in order to calculate the quantum yield, you need to take account of all other possible routes of energy transfer in the excited state, including a variety of possible photophysical and photochemical pathways (intersystem crossing, quenching due to interaction with other species, etc, etc). This makes theoretical estimates of quantum yields terribly complicated. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget*o*ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ On 6/18/2012 21:15, Ram Shankar S ramchemistry2011===gmail.com wrote: Sent to CCL by: "Ram Shankar S" [ramchemistry2011]^[gmail.com] Dear All, I am doing TDDFT calculation of curtain dyes using Gaussian09 software. I would like to know how to calculate quantum yield. Please help me. Thanks in advance With Regards RAAME-mail to subscribers: CHEMISTRY*o*ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net or use ======= ------=_NextPart_000_001D_01CD4ED7.35100570 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

> This makes theoretical estimates of quantum yields terribly = complicated.

 

Yes, but is it not = doable?  Are there any examples where people have attempted to do = theoretical prediction of quantum yields?

 

Jim

 

From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com{=}ccl.net = [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com{=}ccl.net] On = Behalf Of Jens Spanget-Larsen spanget%%ruc.dk
Sent: = Wednesday, June 20, 2012 4:06 AM
To: Kress, Jim =
Subject: CCL:G: how to calculate quantum yield by = computational methods

 

Dear Ram = Shankar!
Theoretical prediction of quantum yields is an extremely = difficult task. The fluorescence quantum yield is a measure of the = fraction of the absorbed number of photons that are emitted by direct = radiative transfer back to the ground state. Hence, in order to = calculate the quantum yield, you need to take account of all other = possible routes of energy transfer in the excited state, including a = variety of possible photophysical and photochemical pathways = (intersystem crossing, quenching due to interaction with other species, = etc, etc). This makes theoretical estimates of quantum yields terribly = complicated.
Yours, Jens = >--<

  =
------------------------------------------------------
  JENS = SPANGET-LARSEN         = Office:      +45 4674 = 2710
  Dept. of Science =
(18.1)     =
Fax:         +45 4674 =
3011
  Roskilde =
University         =
Mobile:      +45 2320 =
6246
  P.O.Box =
260           &nbs=
p;     E-Mail:     spanget*o*ruc.dk
  DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget
  =
------------------------------------------------------

On 6/18/2012 21:15, Ram Shankar S = ramchemistry2011=3D=3D=3Dgmail.com wrote:

Sent to =
CCL by: "Ram Shankar S" =
[ramchemistry2011]^[gmail.com]
Dear =
All,
       I am =
doing TDDFT calculation of curtain dyes using Gaussian09 software. I =
would like to know how to calculate quantum yield. Please help =
me.
 
Thanks in =
advance
 
With =
Regards
RAAME-mail to subscribers: CHEMISTRY*o*ccl.net or =
use:
      http://www.ccl.n=
et/cgi-bin/ccl/send_ccl_message
 
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Before posting, check wait time at: http://www.ccl.net
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&nb=
sp;
 






=3D=3D=3D= =3D=3D=3D=3D
Email scanned by PC Tools - No viruses or spyware = found.
(Email Guard: 9.0.0.888, Virus/Spyware Database: = 6.19950)
http://www.= pctools.com
=3D=3D=3D=3D=3D=3D=3D
=

------=_NextPart_000_001D_01CD4ED7.35100570-- From owner-chemistry@ccl.net Wed Jun 20 13:40:00 2012 From: "Prof. Dr. N. Sekar nethi.sekar^gmail.com" To: CCL Subject: CCL:G: how to calculate quantum yield by computational methods Message-Id: <-47113-120620130608-3999-wtyylTaIwjENN9asqUvHDA:server.ccl.net> X-Original-From: "Prof. Dr. N. Sekar" Content-Type: multipart/alternative; boundary=f46d044787537c776504c2ea69cf Date: Wed, 20 Jun 2012 22:35:54 +0530 MIME-Version: 1.0 Sent to CCL by: "Prof. Dr. N. Sekar" [nethi.sekar.:.gmail.com] --f46d044787537c776504c2ea69cf Content-Type: text/plain; charset=ISO-8859-1 I remember there are some theoretical descriptions. The subject has not grown much in any scientific way further. On Wed, Jun 20, 2012 at 8:54 PM, Jim Kress ccl_nospam###kressworks.com < owner-chemistry:-:ccl.net> wrote: > > This makes theoretical estimates of quantum yields terribly complicated. > **** > > ** ** > > Yes, but is it not doable? Are there any examples where people have > attempted to do theoretical prediction of quantum yields?**** > > ** ** > > Jim**** > > ** ** > > *From:* owner-chemistry+ccl_nospam==kressworks.com**ccl.net [mailto: > owner-chemistry+ccl_nospam==kressworks.com**ccl.net] *On Behalf Of *Jens > Spanget-Larsen spanget%%ruc.dk > *Sent:* Wednesday, June 20, 2012 4:06 AM > *To:* Kress, Jim > *Subject:* CCL:G: how to calculate quantum yield by computational methods* > *** > > ** ** > > Dear Ram Shankar! > Theoretical prediction of quantum yields is an extremely difficult task. > The fluorescence quantum yield is a measure of the fraction of the absorbed > number of photons that are emitted by direct radiative transfer back to the > ground state. Hence, in order to calculate the quantum yield, you need to > take account of all other possible routes of energy transfer in the excited > state, including a variety of possible photophysical and photochemical > pathways (intersystem crossing, quenching due to interaction with other > species, etc, etc). This makes theoretical estimates of quantum yields > terribly complicated. > Yours, Jens >--< > > **** > > ------------------------------------------------------**** > > JENS SPANGET-LARSEN Office: +45 4674 2710**** > > Dept. of Science (18.1) Fax: +45 4674 3011**** > > Roskilde University Mobile: +45 2320 6246**** > > P.O.Box 260 E-Mail: spanget*o*ruc.dk**** > > DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget**** > > ------------------------------------------------------**** > > > On 6/18/2012 21:15, Ram Shankar S ramchemistry2011===gmail.com wrote: **** > > Sent to CCL by: "Ram Shankar S" [ramchemistry2011]^[gmail.com]**** > > Dear All,**** > > I am doing TDDFT calculation of curtain dyes using Gaussian09 software. I would like to know how to calculate quantum yield. Please help me.**** > > ** ** > > Thanks in advance**** > > ** ** > > With Regards**** > > RAAME-mail to subscribers: CHEMISTRY*o*ccl.net or use:******** > > ** ** > > E-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net or use****http://www.ccl.net/chemistry/sub_unsub.shtml**** > > ** ****** > > ** ********** > > ** **http://www.ccl.net/spammers.txt**** > > ** ****** > > ** ** > > ** ** > > > > > > > ======= > Email scanned by PC Tools - No viruses or spyware found. > (Email Guard: 9.0.0.888, Virus/Spyware Database: 6.19950) > http://www.pctools.com > ======= **** > -- Thanks and regards Prof. Dr. N. Sekar CCol FSDC Co-ordinator, UGC-CAS and Professor in Tinctorial Chemistry Dyestuff Technology Department Institute of Chemical Technology (formerly UDCT) Matunga, Mumbai-400019 Mob +91-9867958452 n.sekar:-:ictmumbai.edu.in sekarnm:-:rediffmail.com drnsekar4562000:-:yahoo.co.in website: http://ictmumbai.edu.in/Fac_FacDetails.aspx?fidno=116 --f46d044787537c776504c2ea69cf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I remember there are some theoretical descriptions.=A0 The subject has not = grown much in any scientific way further.

On Wed, Jun 20, 2012 at 8:54 PM, Jim Kress ccl_nospam###kressworks.com <owner-chemistry:-:ccl.net><= /span> wrote:

> This makes theoretical estimates of quantum yields terribly complica= ted.

=A0

Yes, but is= it not doable?=A0 Are there any examples where people have attempted to do= theoretical prediction of quantum yields?

=A0

Jim

=A0

From:= owner-chemistry+ccl_nospam=3D=3Dkressworks.com**ccl.net [mailto:owner-chemistry+ccl_nospam=3D=3D<= a href=3D"http://kressworks.com" target=3D"_blank">kressworks.com**ccl.net] On Behalf Of J= ens Spanget-Larsen spanget%%ruc= .dk
Sent: Wednesday, June 20, 2012 4:06 AM
To: Kress, Jim
= Subject: CCL:G: how to calculate quantum yield by computational meth= ods

=A0

Dear Ram Shankar!
Theoretical predic= tion of quantum yields is an extremely difficult task. The fluorescence qua= ntum yield is a measure of the fraction of the absorbed number of photons t= hat are emitted by direct radiative transfer back to the ground state. Henc= e, in order to calculate the quantum yield, you need to take account of all= other possible routes of energy transfer in the excited state, including a= variety of possible photophysical and photochemical pathways (intersystem = crossing, quenching due to interaction with other species, etc, etc). This = makes theoretical estimates of quantum yields terribly complicated.
Yours, Jens >--<

=A0 -----------=
-------------------------------------------
=A0 JEN=
S SPANGET-LARSEN=A0=A0=A0=A0=A0=A0=A0=A0 Office:=A0=A0=A0=A0=A0 +45 4674 27=
10
=A0 Dept. of Science (18.1)=A0=A0=A0=A0 Fax:=A0=A0=A0=A0=A0=A0=A0=A0 +45 46=
74 3011
=A0 Roskilde University=A0=A0=A0=A0=A0=A0=
=A0=A0 Mobile:=A0=A0=A0=A0=A0 +45 2320 6246
=A0 P.O=
.Box 260=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 E-Mail:=A0=A0=A0=
=A0 spanget*o*ruc.dk<=
/a>
=A0 DK-4000 Roskilde, Denmark=A0=A0 http://www.ruc.dk/~spanget
=A0 ------------------------------------------------------=


On 6/18/2012 21:15, Ram Shankar S ramchemistry2011=3D=3D=3Dgmail.com wrote:

<= pre>Sent to CCL by: "Ram Shankar S" [ramchemistry2011]^[gmail.com]
Dear All,
=A0=A0=A0=A0=A0=A0 I am doing TDDFT =
calculation of curtain dyes using Gaussian09 software. I would like to know=
 how to calculate quantum yield. Please help me.
=A0
Thanks in advance
=A0
=
With Regards
RAAME-mail to subscribers: CHEMISTRY*o*ccl.net or us=
e:
=A0=A0=A0=A0=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=
=A0
E-mail to administrato=
rs: CHEMIS=
TRY-REQUEST*o*ccl.net or use
=A0=A0=A0=A0=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_messa=
ge</ahttp://www.ccl.net/chemistry/sub_unsub.shtml<=
/pre>

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml&l=
t;/ahttp:=
//www.ccl.net/spammers.txt
=A0
RTFI: http://www.=
ccl.net/chemistry/aboutccl/instructions/
=A0
=A0






=3D=3D=3D=3D=3D=3D=3D
Email scanned by PC Tools - No viruses or sp= yware found.
(Email Guard: 9.0.0.888, Virus/Spyware Database: 6.19950)
http:/= /www.pctools.com
=3D=3D=3D=3D=3D=3D=3D




--
Thanks and regards=

Prof. Dr. N. Sekar=A0=A0 CCol FSDC
Co-ordinator, UGC-CAS and Pro= fessor in Tinctorial Chemistry
Dyestuff Technology Department
Institu= te of Chemical Technology (formerly UDCT)
Matunga, Mumbai-400019

Mob +91-9867958452
n.sekar:-:ictmumbai.edu.in
sekarnm:-:rediffmail.= com
drnsekar45= 62000:-:yahoo.co.in
=A0

--f46d044787537c776504c2ea69cf-- From owner-chemistry@ccl.net Wed Jun 20 17:17:00 2012 From: "Adrian Stevens adrian.stevens%x%accelrys.com" To: CCL Subject: CCL: Announcing the release of Accelrys Discovery Studio 3.5 Message-Id: <-47114-120620163907-12396-sWg8F8a/77EqIElgG4L4Xw!A!server.ccl.net> X-Original-From: "Adrian Stevens" Date: Wed, 20 Jun 2012 16:39:05 -0400 Sent to CCL by: "Adrian Stevens" [adrian.stevens*accelrys.com] Accelrys is very pleased to announce the release of the latest version of Discovery Studio 3.5 our most complete and integrated solution for both small molecule and biotherapeutics-based research. Version 3.5 includes many new features and enhancements including: * New Small Molecules Science - New ligand profiling database for drug repurposing or to study side effects - New in-situ fragment-based lead enumeration and scaffold-hopping tools - New Matched Molecular Pairs-based Activity Cliffs analysis * New and Updated Biotherapeutics Science - New Developability Index calculations to rank protein-protein aggregation - New capability to perform pH-dependent mutation energy calculations - Antibody loop modelling enhancements including canonical structure type filtering and updated antibody structure databases - Integration with standard biologics naming schemes: IMGT, Chotia, Honegger, Kabat * Partner Science - CHARMm upgraded to version c36b2 and MODELER upgraded to version 9v10 * Visualization and Performance - Improved toolkit for creating and visualizing receptor-ligand surfaces - Improved support for low specification graphics cards - Updated free DS Visualizer to v3.5 - Updated free 3D plug-in DS ActiveX Control to v3.5 Learn how to accelerate molecular simulations for your drug discovery research, with Discovery Studio 3.5! Register now for our live webinar series at http://accelrys.com/webinars/discovery-studio From owner-chemistry@ccl.net Wed Jun 20 19:49:00 2012 From: "Michael K Gilson mgilson-#-ucsd.edu" To: CCL Subject: CCL: BindingDB News (www.bindingdb.org) Message-Id: <-47115-120620175748-25894-nUxkbFmo0qo53BW4pJ/AZw:server.ccl.net> X-Original-From: "Michael K Gilson" Date: Wed, 20 Jun 2012 17:57:46 -0400 Sent to CCL by: "Michael K Gilson" [mgilson,ucsd.edu] Dear CCL Colleagues, The following recent updates to BindingDB may be of interest: --Easily move data from BindingDB into Excel by downloading a comma-separated value (CSV) file --Zotero users, grab journal citation(s) from the corresponding BindingDB page with a single click --New users: video tutorials to help you get started --Hypothesize protein targets of your favorite bioactive compound(s), based on chemical similarity (http://bit.ly/zX0SfQ) --Use BindingDB to access essentially the complete CNS-relevant PDSP Ki dataset (http://pdsp.med.unc.edu/indexR.html). (Thanks to Brian Roth and coworkers.) --Uniquely access essentially all relevant data from seven chemical biology journals (Nature Chem Biol; ACS Chemical Biol; Chem & Biol; J. Chem Biol; BMC Chem Biol; Chem Biol and Drug Des; Chembiochem) as well as Bioorg Chem and many issues of J. Enz Inhib Med Chem. --Programmatically access BindingDB data via our PSICQUIC server (view here: http://bit.ly/tUtUMr) We hope you find these capabilities useful, and invite your questions and suggestions! Sincerely, Mike Gilson, Tiqing Liu, George Nicola and Linda Hwang Skaggs School of Pharmacy and Pharmaceutical Sciences UC San Diego