From owner-chemistry@ccl.net Wed Aug 2 01:53:00 2006 From: "makowskm]*[chemia.uj.edu.pl" To: CCL Subject: CCL: Radical cation Message-Id: <-32328-060802012157-19448-XxtGrG9GFALF4lDiHRxmcg_+_server.ccl.net> X-Original-From: makowskm!^!chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Wed, 2 Aug 2006 06:39:54 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: makowskm|a|chemia.uj.edu.pl TDDFT can be applied in this case. Standard DFT is also possible provided that the state of interest is the lowest one in a given irreducible representation of symmetry point group. You can get such states if initial guess has proper symmetry and software you use has options to forbid changes in symmetry during SCF iterations. As for literature for the subject you can browse through papers of Grimme, Dierksen or Head-Gordon to mention only few of many active in the area. Regards, Marcin -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm._+_.chemia.uj.edu.pl or Kyushu University email:marcin._+_.cube.kyushu-u.ac.jp > Sent to CCL by: "Mauricio Erben" [erben*quimica.unlp.edu.ar] > Dear CCL subscribers, > > In connection with radical-cation species, I would like to know about the > possibility of calculating another cationic states distinct from the > low-lying one. > > Are excited state or TDDFT methods applicable in these cases? > > Does anyone have some bibliography to suggest dealing with this and > related > issues? > > Thank you very much in advance, > > Mauricio Erben. > > > From owner-chemistry@ccl.net Wed Aug 2 03:02:00 2006 From: "Santosh Khedkar santykhedkar|a|rediffmail.com" To: CCL Subject: CCL: How to make a movie from the trajectory file at Cerius2? Message-Id: <-32329-060801013522-10277-6FSp5qT5fshJ0OD9khptIQ**server.ccl.net> X-Original-From: "Santosh Khedkar" Content-type: multipart/alternative; boundary="Next_1154406777---0-202.54.124.152-26383" Date: 1 Aug 2006 04:32:58 -0000 MIME-Version: 1.0 Sent to CCL by: "Santosh Khedkar" [santykhedkar%x%rediffmail.com] This is a multipart mime message --Next_1154406777---0-202.54.124.152-26383 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Jun,=0AThe Windows movie maker will help you.=0ASantosh =0A=0A=0AOn Tue,= 01 Aug 2006 Jun Zhao jzhao#,#tamu.edu wrote :=0A>Sent to CCL by: "Jun Zha= o" [jzhao|-|tamu.edu]=0A>Does anyone know how to make a movie from the traj= ectory file? I got the trajectory file from the molecular dynamics simulati= on at Cerius 2. I want to make a short movie based on the trajectory file s= o that I can play it in the powerpoint presentation. Any suggestion is grea= tly appreciated.=0A>=0A>Jun Zhao=0A>=0A>Ph.D. Candidate=0A>Dept of Atmosphe= ric Sciences=0A>Texas A&M University=0A>College Station, TX 77843=0A>Office= : (979) 458-0555=0A>Fax: (979) 862-4466=0A>=0A>=0A>=0A>-=3D This is automat= ically added to each message by the mailing script =3D-=0A>To recover the e= mail address of the author of the message, please change=0A>the strange cha= racters on the top line to the ^ sign. You can also=0A>look up the X-Origin= al-From: line in the mail header.=0A>=0A>E-mail to subscribers: CHEMISTRY^c= cl.net or use:=0A=0A= >=0A=0A> h= ttp://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A>=0A>Subscribe/Unsubscribe= :=0A=0A>=0A>Before post= ing, check wait time at: http://www.ccl.net=0A>=0A>Job: http://www.ccl.net/= jobs=0A>Conferences: http://server.ccl.net/chemistry/announcements/conferen= ces/=0A>=0A>Search Messages: http://www.ccl.net/htdig (login: ccl, Passwor= d: search)=0A>=0A=0A==0A>=0A>RTFI: http://www.ccl.net/che= mistry/aboutccl/instructions/=0A>=0A>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+=0A>=0A>=0A>=0A=0A=0ASANTOSH AMBADAS KHED= KAR=0D=0A=0D=0AComputer-Aided Molecular Design Lab=0D=0ADepartment of Pharm= aceutical Chemistry=0D=0ABombay College of Pharmacy=0D=0AKalina, Santacruz = (E), Mumbai-400 098=0D=0AMobile: 09322834634. Home:02447-244064.=0D=0A-----= ---------------------------------------------------------------------------= ----------------------------------------=0D=0A"When one door of happiness c= loses, another opens; but often we look so long at the=0D=0Aclosed door tha= t we do not see the one which has opened for us" --Helen Keller=0D=0A******= ***************************************************************************= **************** --Next_1154406777---0-202.54.124.152-26383 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0AHi Jun,
=0AThe Windows movie maker will help you.
=0ASantosh =0A
=0A
=0AOn Tue, 01 Aug 2006 Jun Zhao jzhao#,#tamu.edu wrote :=0A>Sent to CCL by: "Jun  Zhao" [jzhao|-|tamu.edu]
= =0A>Does anyone know how to make a movie from the trajectory file? I got= the trajectory file from the molecular dynamics simulation at Cerius 2. I = want to make a short movie based on the trajectory file so that I can play = it in the powerpoint presentation. Any suggestion is greatly appreciated.=0A>
=0A>Jun Zhao
=0A>
=0A>Ph.D. Candidate
=0A>= ;Dept of Atmospheric Sciences
=0A>Texas A&M University
=0A>= College Station, TX 77843
=0A>Office: (979) 458-0555
=0A>Fax: (= 979) 862-4466
=0A>
=0A>
=0A>
=0A>-=3D This is autom= atically added to each message by the mailing script =3D-
=0A>To reco= ver the email address of the author of the message, please change
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=0A>-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
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=0A=0A=0ASANTOSH AMBADAS KHEDKAR=0D=0A=0D
=0AComputer-Aided Molecular Design Lab=0D
=0ADepartment = of Pharmaceutical Chemistry=0D
=0ABombay College of Pharmacy= =0D
=0AKalina, Santacruz (E), Mumbai-400 098=0D
=0AMobile: = 09322834634. Home:02447-244064.=0D
=0A-----------------------------= ---------------------------------------------------------------------------= ----------------=0D
=0A"When one door of happiness closes,&nbs= p;another opens; but often we look so long at the=0D=0Aclosed door that we do not see the one which h= as opened for us" --Helen Keller=0D
=0A***********************= **************************************************************************<= br>
=0A=0A --Next_1154406777---0-202.54.124.152-26383-- From owner-chemistry@ccl.net Wed Aug 2 04:28:01 2006 From: "Tarek Ma amon El Gogary asmasomy~~mans.edu.eg" To: CCL Subject: CCL:G: complexation energy Message-Id: <-32330-060801132750-28064-SDmXg4waXONCGSOANS/uoQ^^^server.ccl.net> X-Original-From: "Tarek Ma amon El Gogary" Date: Tue, 1 Aug 2006 13:27:09 -0400 Sent to CCL by: "Tarek Ma amon El Gogary" [asmasomy---mans.edu.eg] Hello Yunusa, To the best of my knowledge, there is no direct way (Gaussian keyword) to calculate the complexation energy. what we normally do is to calculate the energy of the complexation reaction which can be done as the sum of the energies of the optimized geometry of the products minus that of the reactants. I hope that could be of help to you. Good luck Dr Tarek ElGogary Jazan Teacher's college KSA From owner-chemistry@ccl.net Wed Aug 2 15:35:00 2006 From: "Eugen Leitl eugen-*-leitl.org" To: CCL Subject: CCL: Gromacs tutorial Message-Id: <-32331-060802012157-1234-pzT5OgVGz/sw5S9TD+XpSQ .. server.ccl.net> X-Original-From: Eugen Leitl Date: Wed, 2 Aug 2006 18:32:11 +0200 Sent to CCL by: Eugen Leitl [eugen..leitl.org] Clustermonkey just published a very nice Gromacs tutorial by Erik Lindahl: http://www.clustermonkey.net//content/view/141/33/ -- Eugen* Leitl http://leitl.org ______________________________________________________________ ICBM: 48.07100, 11.36820 http://www.ativel.com 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE From owner-chemistry@ccl.net Wed Aug 2 17:25:00 2006 From: "Mateusz Witkowski big_mateo-,-inbox.com" To: CCL Subject: CCL: Thermodynamics and equilibrium Message-Id: <-32332-060802172304-27941-q0C9f5tn2LtoSpUI7fbvmA#,#server.ccl.net> X-Original-From: Mateusz Witkowski Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=US-ASCII Date: Wed, 2 Aug 2006 13:22:53 -0800 Mime-Version: 1.0 Sent to CCL by: Mateusz Witkowski [big_mateo|,|inbox.com] Hello CCl-ers, Due to vacations I was unable to thank you for all the answers related to my question about lone pairs. I still have some doubts but meanwhile I need your assistance in another topic. I've just finished a QM based investigation of some reaction. As a result I've obtained two pathways that differ mainly in the activation energy barriers. R1) A <--> Ts1 <--> INT <--> Ts2 <--> A' E= 0 22 15 27 6 R2) A <--> Ts1 <--> INT <--> Ts2 <--> A' E= 0 27 24 28 19 In the case of R2, there is a significant difference between A and A' and the Ea for TS2 is "only" 9kcal/mol so it seems that equilibrium is definitely shifted towards A. What about R1? The difference between A and A' is 6kcal/mol but both Ea for Ts1 and Ts2 are more than 20kcal/mol - can I think of equilibrium or maybe just about the comparable likelihood of both forms. Second question - I would like to calculate rate constants for these reactions based on TS theory. Should I consider A -- TS2 -- A'? Last question - what is the reasonable height of the activation barrier for the biological system? As always - TIA Mateo