From owner-chemistry@ccl.net Fri Nov 3 08:11:00 2006 From: "Igor Avilov avilovi]=[averell.umh.ac.be" To: CCL Subject: CCL: TDDFT-populations Message-Id: <-32933-061103080710-14200-HRt02wi6rU1oYmJTjOJirw|,|server.ccl.net> X-Original-From: "Igor Avilov" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 3 Nov 2006 14:13:47 +0100 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi=averell.umh.ac.be] Dear Matthew, Look at the following reference: Dreuw, A.; Head-Gordon, M. Chem. Rev. 2005, 105, 4009-4037 Best regards, Igor. -----Original Message----- > From: owner-chemistry() ccl.net [mailto:owner-chemistry() ccl.net] Sent: mercredi 1 novembre 2006 18:27 To: Igor Avilov Subject: CCL: TDDFT-populations Sent to CCL by: "matthew tassell" [mjt22{=}sussex.ac.uk] Dear All, when using Gaussain 03 to perform TDDFT calculations i noticed that in the output you get excitation energies and oscillator strengths and no other information. I was wondering if perhaps anybody knew of a way to get information about the excited state electron configuration? so that i would be able work out which electron has performed the transition. Any insight gratefully recieved, matthttp://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 Fri Nov 3 08:46:01 2006 From: "Igor Avilov avilovi..averell.umh.ac.be" To: CCL Subject: CCL:G: UV Spectra Calculation using Gaussian03 Message-Id: <-32934-061103081000-14391-XWXgvD4UZrdoGA5ohIEz0g_._server.ccl.net> X-Original-From: "Igor Avilov" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 3 Nov 2006 14:16:50 +0100 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi(~)averell.umh.ac.be] Dear Atilio, You should look at the nature of the excited states of interest. If it is mostly HOMO-to-LUMO excitation, than, on my opinion, the energy shift of this transition can be related to the change of the HOMO/LUMO gap. Best regards, Igor. -----Original Message----- > From: owner-chemistry..ccl.net [mailto:owner-chemistry..ccl.net] Sent: mercredi 1 novembre 2006 20:46 To: Igor Avilov Subject: CCL:G: UV Spectra Calculation using Gaussian03 Sent to CCL by: Atilio I Anzellotti/O/VCU [aanzellotti~~vcu.edu]
Dear All,
 
   Regarding calcu= lation of UV spectra with gaussian 03, I have used DFT to optimize the geom= etry of some free and platinated nucleobases, the energy HOMO/LUMO gap = ;is showing a smaller separation for the platinated compared to the fr= ee ones. I can see this shift in the UV absorption maxima. Could I proposed= a direct correlation between calculated HOMO/LUMO gaps and experimental re= sults?
 
Many Thanks.
 
A= tilio.
-----owner-chemistry.:.ccl.net wrote: -= ----

To= : "Anzellotti, Atilio " <aanzellotti.:.vcu.edu>
From: "Shobe= , David David.Shobe()sud-chemie.com" <owner-chemistry.:.ccl.net>
Sen= t by: owner-chemistry.:.ccl.net
Date: 10/31/2006 02:45PM
Subject: CCL:G= : UV Spectra Calculation using Gaussian03

Sent to CCL by: "Shobe, David= " [David.Shobe-x-sud-chemie.com]

Unfortunately, none of the methods = in Gaussian will give you an actual
spectrum (i.e. a continuous graph of= absorbance v. wavelength).  All you
will get are energy levels and= transition moments.  

To the list: is there a program that wil= l calculate actual spectra?
Nothing was available when I last asked (abo= ut five years ago) but maybe
that's changed.

--David Shobe

-----Original Message-----
> From: owner-chemistry!A!ccl.net [mailto:owner-chem= istry!A!ccl.net]
Sent: Tuesday, October 31, 2006 2:22 AM
To: Sho= be, David
Subject: CCL:G: UV Spectra Calculation using Gaussian03
Sent to CCL by: "Young  Leh" [youngleh=5F+=5Fgmail.com] I am planing = to
calculate UV spectra using Gaussian03.  I found "TD" is keyword = to go
> from the manual but it does not state clearly how to use it.<= BR>
B3LYP/6-31G* TD

UV Spectra

molecular specification

Can I extract the info Absorbance vs. Lamda and compare with
ex= eprimental spectra?

Thankshttp://www.ccl.net/cgi-bin/ccl/send=5Fccl= =5Fmessagehttp://www.ccl.net/chemistry/sub=5Funsub.shtmlhttp://www.ccl.net/= spammers.txtThis e-mail message may contain confidential and / or privilege= d information. If you are not an addressee or otherwise authorized to recei= ve this message, you should not use, copy, disclose or take any action base= d on this e-mail or any information contained in the message. If you have r= eceived this material in error, please advise the sender immediately by rep= ly e-mail and delete this message.
Thank you.



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=http://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 Fri Nov 3 14:47:01 2006 From: "Mireille Krier mv.krier[*]googlemail.com" To: CCL Subject: CCL: Halogen atoms interactions Message-Id: <-32935-061103025254-16633-ec560bvR4haebhExvjWupQ|-|server.ccl.net> X-Original-From: "Mireille Krier" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=WINDOWS-1252; format=flowed Date: Fri, 3 Nov 2006 07:57:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Mireille Krier" [mv.krier^_^googlemail.com] Dear Olivier, please have a look at the following two references : - Halogen bonds in biological molecules. Auffinger P, Hays FA, Westhof E, Shing Ho P (2004) Proc Nat Acad Sci 101:16789–16794 http://dx.doi.org/10.1073/pnas.0407607101 - An overview of halogen bonding. Peter Politzer , Pat Lane, Monica C. Concha, Yuguang Ma and Jane S. Murray; Journal of Molecular Modeling(2006) http://dx.doi.org/10.1007/s00894-006-0154-7 Cheers, Mireille On 11/2/06, olivier sperandio olivier.sperandio]=[univ-paris5.fr wrote: > Sent to CCL by: "olivier sperandio" [olivier.sperandio++univ-paris5.fr] > Does anybody know key publications about the specific role of halogen atoms (I,Br,Cl,F) in protein/ligand complexes ? > > Olivier Sperandio. > Ph.D. student > University of Paris 5 - Rene Descartes > > olivier.sperandio**univ-paris5.fr From owner-chemistry@ccl.net Fri Nov 3 21:32:00 2006 From: "Delwar Hossain hossaind2004 . yahoo.com" To: CCL Subject: CCL:G: How to keep the position of an atom fixed? Message-Id: <-32936-061103212522-2477-leDWIcBBsCxz1Ipre6cvIQ:_:server.ccl.net> X-Original-From: Delwar Hossain Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1944507018-1162603515=:2802" Date: Fri, 3 Nov 2006 17:25:15 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Delwar Hossain [hossaind2004/./yahoo.com] --0-1944507018-1162603515=:2802 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear All, I am planing to calculate the energy of a molecule keeping an atom in different fixed position by using Gaussian 03. More precisely let a molecule A and an atom B. Atom B will be set in different position relative to the center of molecule B. I want to calculate the interaction energy between A and B where the postion of B will remain same.How can I keep the position of B fixed? I appreciate your generous help. Thank you. With regards, Sincerely yours, Delwar Hossain Mississippi State University --------------------------------- Everyone is raving about the all-new Yahoo! Mail. --0-1944507018-1162603515=:2802 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear All,
I am planing to calculate the energy of a molecule  keeping an atom in different fixed position by using Gaussian 03. More precisely let a molecule A and an atom B. Atom B will be set in different position relative to the center of molecule B. I want to calculate the interaction energy between A and B where the postion of B will remain same.How can I keep the position of B fixed?
I appreciate your generous help.
Thank you.
With regards,
Sincerely yours,
Delwar Hossain
Mississippi State University
 

Everyone is raving about the all-new Yahoo! Mail. --0-1944507018-1162603515=:2802-- From owner-chemistry@ccl.net Fri Nov 3 22:06:00 2006 From: "Jeff Nauss jnauss^accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for December 2006 Message-Id: <-32937-061103204737-1045-McAE+cC9uK+BECo5KzrWHQ%server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Fri, 3 Nov 2006 16:43:38 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss[]accelrys.com] Accelrys Inc. are holding the following training workshops during December 2006. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the scheduled workshops are $500 per day for all customers. For the on-line presentations, the price is $175 per three hour session for all customers. SAN DIEGO, CA, USA Introduction to Life Science Modeling with InsightII 5 - 6 Dec Homology-Based Protein Design 7 - 8 Dec CHARMm 11 - 12 Dec Structure Based Drug Design with InsightII 13 - 14 Dec BURLINGTON, MA, USA Protein Modeling in Discovery Studio 5 Dec Simulations in Discovery Studio 6 Dec Structure-Based Design in Discovery Studio 7 Dec ONLINE TRAINING MacVector 13 Dec (3pm PST) MacVector 14 Dec (7am PST) Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html and http://www.accelrys.com/services/training/general/calendar_online.html. Questions regarding scheduling and content should be directed to workshops++accelrys.com. -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training From owner-chemistry@ccl.net Fri Nov 3 23:54:00 2006 From: "SOREN EUSTIS soren\a/jhu.edu" To: CCL Subject: CCL:G: How to keep the position of an atom fixed? Message-Id: <-32938-061103235141-19855-2NbaQmdzjXHCm+8GjNpz2w%server.ccl.net> X-Original-From: SOREN EUSTIS Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Fri, 03 Nov 2006 23:51:35 -0500 MIME-version: 1.0 Sent to CCL by: SOREN EUSTIS [soren[-]jhu.edu] This is easy to set up in GaussView. Just use the Redundant coordinate editor. Set one coordinate to be frozen and scan the other coordinate. See this example for molecular oxygen: %chk=o2.chk %mem=6MW %nproc=1 # hf/6-31++g(d,p) geom=(modredundant,connectivity) Oxygen Energy Scan 0 1 O O 1 B1 B1 1.16160000 1 2 2.0 2 X 1 F B 2 1 0.500000 S 100 0.010000 The last two entries specify that atom 1 is Fixed and that the Bond between 2 and 1 is to be set at 0.5 A, scanned in 0.01A increments 100 times. Soren N. Eustis Graduate Research Assistant Department of Chemistry Johns Hopkins University Remsen Hall 3400 N Charles Street Baltimore, MD 21218 (410) 516-4675 (office) (410) 925-5167 (cell) (410) 516-8420 (fax) soren ~ jhu.edu -----Original Message----- > From: owner-chemistry ~ ccl.net [mailto:owner-chemistry ~ ccl.net] Sent: Friday, November 03, 2006 9:46 PM To: Eustis, Soren Subject: CCL:G: How to keep the position of an atom fixed? Sent to CCL by: Delwar Hossain [hossaind2004/./yahoo.com] --0-1944507018-1162603515=:2802 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear All, I am planing to calculate the energy of a molecule keeping an atom in different fixed position by using Gaussian 03. More precisely let a molecule A and an atom B. Atom B will be set in different position relative to the center of molecule B. I want to calculate the interaction energy between A and B where the postion of B will remain same.How can I keep the position of B fixed? I appreciate your generous help. Thank you. With regards, Sincerely yours, Delwar Hossain Mississippi State University