From chemistry-request@server.ccl.net Fri Mar 2 04:32:58 2001 Received: from localhost.ox.ac.uk (root@baaden.biop.ox.ac.uk [163.1.16.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f229Wvw03149 for ; Fri, 2 Mar 2001 04:32:57 -0500 Received: from smplinux.de (baaden@localhost [127.0.0.1]) by localhost.ox.ac.uk (8.9.3/8.9.3/Debian 8.9.3-21) with ESMTP id JAA24135 for ; Fri, 2 Mar 2001 09:32:57 GMT Message-Id: <200103020932.JAA24135@localhost.ox.ac.uk> X-Authentication-Warning: localhost.ox.ac.uk: Host baaden@localhost [127.0.0.1] claimed to be smplinux.de X-Mailer: exmh version 2.1.1 10/15/1999 (debian) To: CHEMISTRY@ccl.net Subject: Hardware question: dials for Linux ? X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-Face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Fri, 02 Mar 2001 09:32:57 +0000 From: Marc BAADEN Hi, as I have almost completely switched to a Linux based workstation, I wonder wether SGI-like dial boxes are available and supported for these platforms. I am particularly interested in using them with rasmol, so if anybody can report wether dial boxes under linux work successfully with that software, I would be very grateful. Reports for any other (mainly visualisation/mol. modeling) software under linux which supports dial box hardware would also be appreciated. Thank you in advance, Best regards, Marc Baaden -- Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de FAX/Voice +49 40333 968508 - Tel: +44 1865 275380 or +33 609 843217 From chemistry-request@server.ccl.net Thu Mar 1 23:52:41 2001 Received: from web6203.mail.yahoo.com (web6203.mail.yahoo.com [128.11.22.114]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f224qfw00845 for ; Thu, 1 Mar 2001 23:52:41 -0500 Message-ID: <20010302045241.11823.qmail@web6203.mail.yahoo.com> Received: from [172.146.1.223] by web6203.mail.yahoo.com; Thu, 01 Mar 2001 20:52:41 PST Date: Thu, 1 Mar 2001 20:52:41 -0800 (PST) From: Iraj Daizadeh Subject: Re: CCL:ET theory/Electronic coupling To: "Hui-Hsu \(Gavin\) Tsai" , chemistry@ccl.net Cc: silmar@tbi.univie.ac.at, Chia-Pin Pan , plin@mail.chem.tamu.edu In-Reply-To: <009301c0a272$53c0f560$67811681@cwru.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. Please see the paper of Stuchebrukhov at UC Davis; TDA (not HDA) has been compared with experiment. http://www-chem.ucdavis.edu/groups/stuchebrukhov/publications.html http://www-chem.ucdavis.edu/people/stuchebrukhov.shtml For the assumptions, see spin-boson model ( a nice discussion by Shulten at UIUC)... best wishes, iraj. --- "Hui-Hsu (Gavin) Tsai" wrote: > Dear CCLers and Silmar: > > Thanks for Silmar's email. It is very > helpful. > > The two assumptions Silmar pointed out answer > part of my questions. > > ** [The most common electron transfer theories use > the two > following assumptions: > (i) The electronic coupling(Tab) is >> than > the other therms. > (ii) Tab(Q)=Tab(Q*), i.e, the value of Tab > is constant and is > equal to the one obtained for the > transition state (TS).]** > > From Marcus theory, the factors which can > affect ET rate are electronic > coupling, temperature, driving force (G), and > reorganization energy. Some > researches are mainly focused on the theoretical > calculations (superexchange > and NBO analysis) of electronic coupling. (Newton, > Ratner, Curtiss, Miller, > Paddon-Row...) > (Maybe) Due to these two assumptions, the other > factors are ignored. > The one interesting point in these researches is > most of the calculated > data are not compared with experimental results. As > usual, most theoretical > calculations are compared with well-known results to > assess the quality. > > The another interesting question is different > experimental methods. > They are several spectroscopic methods are used to > measure the ET rate such > as time-resolved fluorescence, ultrafast absorption > different > spectroscopy, and transient absorption... > I even think some measured rates are not involved > with the nuclear > reorganization and solvent reorientation > and the electronic coupling dominates the rate due > to the fast time scale. > There are also some different kinds of electron > transfer such as pohotinduced > excited state electron transfer and gound state > charge/hole hopping. > I also think different measurement of different > kinds of electron transfer > shall require different theoretical approaches. But > the concepts are not > clear for me. > > I am just the beginner of this field. Any > discussion and comment are > valuable, welcome, and appreciated. > > Gavin > > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | > Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Fri Mar 2 08:22:45 2001 Received: from icod.ccti.ull.es (icod.ccti.ull.es [193.145.120.37]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f22DMiw06214 for ; Fri, 2 Mar 2001 08:22:44 -0500 Received: from ull.es (unknown [193.145.106.38]) by icod.ccti.ull.es (Postfix) with ESMTP id 66BB54192 for ; Fri, 2 Mar 2001 13:22:42 +0000 (UCT) Message-ID: <3A9F9D22.DAC8672B@ull.es> Date: Fri, 02 Mar 2001 13:16:18 +0000 From: Pilar Carro Reply-To: pcarro@ull.es Organization: Dpto Quimica Fisica X-Mailer: Mozilla 4.5 [es] (Win98; I) X-Accept-Language: es MIME-Version: 1.0 To: chemistry@ccl.net Subject: Effective Core Potential for gold Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I am interested to know if there exits the possibility in Gaussian98 to describe a gold atom with only a single outer s electron and the remainder of the atomic electron density described by a efective core potential. What type of ECP I must use in this case? and what is the way I must introduce this ECP in the gaussian job file?. I would appreciate any help from you Thanks in advance, P.Carro (pcarro@ull.es) From chemistry-request@server.ccl.net Fri Mar 2 11:47:31 2001 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f22GlSw08917 for ; Fri, 2 Mar 2001 11:47:29 -0500 Received: from lauca.usach.cl ([158.170.51.105]) by lauca.usach.cl (8.10.0.Beta12/8.10.0.Beta10) with ESMTP id f22GiHe02972 for ; Fri, 2 Mar 2001 13:44:17 -0300 (CDT) Message-ID: <3A9FCF96.7C85A18F@lauca.usach.cl> Date: Fri, 02 Mar 2001 13:51:34 -0300 From: Danilo Gonzalez X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Ligand binding to protein (DeltaH=0) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi folks! I'm looking for references about systems where ligand binding to protein is carried out with Delta H = 0, that is, where the process is Entropically driven. Thanks a lot for any reference! Danilo Gonzalez Univeristy of Santiafo de Chile Facultad de Quimica y Biologia From chemistry-request@server.ccl.net Fri Mar 2 12:43:16 2001 Received: from bilbo.edu.uy ([164.73.160.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f22HhDw09757 for ; Fri, 2 Mar 2001 12:43:14 -0500 Received: from [164.73.160.178] (inorganica-03.fq.edu.uy [164.73.160.178]) by bilbo.edu.uy (8.11.0/8.11.0) with SMTP id f22Hgs121564 for ; Fri, 2 Mar 2001 14:42:54 -0300 Message-Id: <200103021742.f22Hgs121564@bilbo.edu.uy> Comments: hostname=bilbo canonical_name=bilbo.edu.uy domain_name=edu.uy Comments: Date=Fri, 2 Mar 2001 14:42:54 -0300 Ident=inorganica-03.fq.edu.uy [164.73.160.178] To: "chemistry@ccl.net" Subject: CCL: theoretical study of rhenium complexes in aqueous solution Date: Fri, 02 Mar 01 14:47:21 -0500 From: Jorge Gancheff X-Mailer: E-Mail Connection v2.5.03 -- [ From: Jorge Gancheff * EMC.Ver #2.5.02 ] -- Dear CCLŽers, IŽm looking for references about ab initio or DFT study of rhenium (or technetium) complexes in aqueous solution. I would appreciate any help from you. Thanks in advance, Jorge Gancheff (jorge@bilbo.edu.uy) Faculty of Chemistry, UdelaR, Uruguay -- From chemistry-request@server.ccl.net Fri Mar 2 12:58:04 2001 Received: from web11603.mail.yahoo.com (web11603.mail.yahoo.com [216.136.172.55]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f22Hw3w10084 for ; Fri, 2 Mar 2001 12:58:03 -0500 Message-ID: <20010302175802.37424.qmail@web11603.mail.yahoo.com> Received: from [63.97.7.140] by web11603.mail.yahoo.com; Fri, 02 Mar 2001 09:58:02 PST Date: Fri, 2 Mar 2001 09:58:02 -0800 (PST) From: Jianxin Guo Subject: Re: ET theory/Electronic coupling To: hxt10@po.cwru.edu Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Gavin, The ET theory has been developped pretty so far compared with experimental results. There are thoudands of paper for this kind of comparison. several good review papers are: 1. newton, MD, quantum chemical probes of electron-transfer kietics - the nature of donor acceptor interactions. chemical reviews,1991,91,767-792 2. parbara,pf; meyer tj; ratner ma, contemporary issues in electron transfer research. journal of physical chemistry,1996,100,13148-13168. Some recently developped novel methods was not reviewed in those papers, for examples, 3. Stuchebrukhov,AA. tunneling currents in long-distance electron transfer reactions. III. many-electron formulation. Journal of chemical physics,1998,108,8499-8509 Those methods have been programmed, you can contact with Dr. Stuchebrukhov for those codes. There are also many other excellent papers, which I did not list here. Enjoy your exploring in ET fields. Jianxin > From chemistry-request@server.ccl.net Thu Mar 1 Message-ID: <009301c0a272$53c0f560$67811681@cwru.edu> Reply-To: "Hui-Hsu (Gavin) Tsai" From: "Hui-Hsu (Gavin) Tsai" To: Cc: , "Chia-Pin Pan" , Subject: ET theory/Electronic coupling Date: Thu, 1 Mar 2001 12:09:02 -0500 Dear CCLers and Silmar: Thanks for Silmar's email. It is very helpful. The two assumptions Silmar pointed out answer part of my questions. ** [The most common electron transfer theories use the two following assumptions: (i) The electronic coupling(Tab) is >> than the other therms. (ii) Tab(Q)=Tab(Q*), i.e, the value of Tab is constant and is equal to the one obtained for the transition state (TS).]** From Marcus theory, the factors which can affect ET rate are electronic coupling, temperature, driving force (G), and reorganization energy. Some researches are mainly focused on the theoretical calculations (superexchange and NBO analysis) of electronic coupling. (Newton, Ratner, Curtiss, Miller, Paddon-Row...) (Maybe) Due to these two assumptions, the other factors are ignored. The one interesting point in these researches is most of the calculated data are not compared with experimental results. As usual, most theoretical calculations are compared with well-known results to assess the quality. The another interesting question is different experimental methods. They are several spectroscopic methods are used to measure the ET rate such as time-resolved fluorescence, ultrafast absorption different spectroscopy, and transient absorption... I even think some measured rates are not involved with the nuclear reorganization and solvent reorientation and the electronic coupling dominates the rate due to the fast time scale. There are also some different kinds of electron transfer such as pohotinduced excited state electron transfer and gound state charge/hole hopping. I also think different measurement of different kinds of electron transfer shall require different theoretical approaches. But the concepts are not clear for me. I am just the beginner of this field. Any discussion and comment are valuable, welcome, and appreciated. Gavin __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Fri Mar 2 13:56:28 2001 Received: from usc.edu (root@usc.edu [128.125.253.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f22IuRw10655 for ; Fri, 2 Mar 2001 13:56:27 -0500 Received: from chem1.usc.edu (chem1.usc.edu [128.125.8.55]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id KAA21565; Fri, 2 Mar 2001 10:56:16 -0800 (PST) Received: from usc.edu (kenitra.usc.edu [128.125.14.38]) by chem1.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id KAA06408; Fri, 2 Mar 2001 10:56:14 -0800 Message-ID: <3A9FF0F5.15ACAA07@usc.edu> Date: Fri, 02 Mar 2001 11:13:57 -0800 From: Jordi Villa X-Mailer: Mozilla 4.72 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Iraj Daizadeh CC: "Hui-Hsu (Gavin) Tsai" , chemistry@ccl.net, silmar@tbi.univie.ac.at, Chia-Pin Pan , plin@mail.chem.tamu.edu Subject: Re: CCL:ET theory/Electronic coupling References: <20010302045241.11823.qmail@web6203.mail.yahoo.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi there, At this point of the discussion I would like to add two references on the treatment of ET in the condensed phase with the dispersed polaron approach. I hope this is useful information. @article{warshel86a, Author = {Warshel, A. and Hwang, J.-K.}, Title = {Simulation of the Dynamics of Electron Transfer Reactions in Polar Solvents: Semiclassical Trajectories and Dispersed Polaron Approaches}, Journal = JCP, Volume = {84}, Pages = {4938-4957}, Year = {1986} } @article{warshel89a, Author = {Warshel, A. and Chu, Z. T. and Parson, W. W.}, Title = {Dispersed Polaron Simulations of Electron Transfer in Photosynthetic Reaction Centers}, Journal = {Science}, Volume = {246}, Pages = {112-116}, Year = {1989} } Iraj Daizadeh wrote: > Hello. > > Please see the paper of Stuchebrukhov at UC Davis; > TDA (not HDA) has been compared with experiment. > > http://www-chem.ucdavis.edu/groups/stuchebrukhov/publications.html > http://www-chem.ucdavis.edu/people/stuchebrukhov.shtml > > For the assumptions, see spin-boson model ( a nice > discussion by Shulten at UIUC)... > > best wishes, iraj. > > --- "Hui-Hsu (Gavin) Tsai" wrote: > > Dear CCLers and Silmar: > > > > Thanks for Silmar's email. It is very > > helpful. > > > > The two assumptions Silmar pointed out answer > > part of my questions. > > > > ** [The most common electron transfer theories use > > the two > > following assumptions: > > (i) The electronic coupling(Tab) is >> than > > the other therms. > > (ii) Tab(Q)=Tab(Q*), i.e, the value of Tab > > is constant and is > > equal to the one obtained for the > > transition state (TS).]** > > > > From Marcus theory, the factors which can > > affect ET rate are electronic > > coupling, temperature, driving force (G), and > > reorganization energy. Some > > researches are mainly focused on the theoretical > > calculations (superexchange > > and NBO analysis) of electronic coupling. (Newton, > > Ratner, Curtiss, Miller, > > Paddon-Row...) > > (Maybe) Due to these two assumptions, the other > > factors are ignored. > > The one interesting point in these researches is > > most of the calculated > > data are not compared with experimental results. As > > usual, most theoretical > > calculations are compared with well-known results to > > assess the quality. > > > > The another interesting question is different > > experimental methods. > > They are several spectroscopic methods are used to > > measure the ET rate such > > as time-resolved fluorescence, ultrafast absorption > > different > > spectroscopy, and transient absorption... > > I even think some measured rates are not involved > > with the nuclear > > reorganization and solvent reorientation > > and the electronic coupling dominates the rate due > > to the fast time scale. > > There are also some different kinds of electron > > transfer such as pohotinduced > > excited state electron transfer and gound state > > charge/hole hopping. > > I also think different measurement of different > > kinds of electron transfer > > shall require different theoretical approaches. But > > the concepts are not > > clear for me. > > > > I am just the beginner of this field. Any > > discussion and comment are > > valuable, welcome, and appreciated. > > > > Gavin > > > > > > -= This is automatically added to each message by > > mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | > > CHEMISTRY-REQUEST@ccl.net -- To Admins > > CHEMISTRY-SEARCH@ccl.net -- archive search | > > Gopher: gopher.ccl.net 70 > > Ftp: ftp.ccl.net | WWW: > > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > > > > > __________________________________________________ > Do You Yahoo!? > Get email at your own domain with Yahoo! Mail. > http://personal.mail.yahoo.com/ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Jordi Villa Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil From chemistry-request@server.ccl.net Fri Mar 2 15:33:25 2001 Received: from hotmail.com (f240.law10.hotmail.com [64.4.15.240]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f22KXPw11540 for ; Fri, 2 Mar 2001 15:33:25 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 2 Mar 2001 12:33:26 -0800 Received: from 128.97.139.222 by lw10fd.law10.hotmail.msn.com with HTTP; Fri, 02 Mar 2001 20:33:25 GMT X-Originating-IP: [128.97.139.222] From: "hu eric" To: chemistry@ccl.net Subject: software to detect binding site Date: Fri, 02 Mar 2001 12:33:25 -0800 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312; format=flowed Message-ID: X-OriginalArrivalTime: 02 Mar 2001 20:33:26.0055 (UTC) FILETIME=[08729370:01C0A358] Dear CCLers I'm working on a big protein which has multiple binding domains. Is there a way to choose the best binding site for the ligand? Maybe it's just a dream. Eric _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com.