From owner-chemistry@ccl.net Fri Mar 3 00:23:01 2006 From: "Raji Raji raji(0)anal.chem.tohoku.ac.jp" To: CCL Subject: CCL: ORCA Message-Id: <-31092-060303001745-19039-LHHyMzkRl6ckxkvuLVGRLA-$-server.ccl.net> X-Original-From: "Raji Raji" Date: Fri, 3 Mar 2006 00:17:44 -0500 Sent to CCL by: "Raji Raji" [raji . anal.chem.tohoku.ac.jp] Dear CCL Members, Can you please explain me the following doubts regarding ORCA calculations: 1) For TDDFT/TDA calculations with B3LYP/6-311G (using ORCA), in the COSMO part, I have to mention both solvent dielectric constant and refractive index? or just dielectric constant is enough? Its given in the manual that the refractive index is used only for CIS or MRCI modules. Since in ORCA, CIS keyword is applicable for both CIS and TDDFT calculations, I got confused. So the refractive index is also necessary for TDDFT/TDA with hybrid functionals? By the way I am using RI approximation too. 2) When I use RI approximation (RIJONX for the same hybrid function and basis set), it will only be applied to the Coulomb term; so does it mean no need to specify the auxiliary basis for the coulomb term and should be specified only for the correlation calculations? In this case using SV/C as an auxiliary basis set is a valid option or not? If it is valid one, then is it a good choice for the accurate calculations? 3) When I do population analysis, I want to analyse the results using molekel. so in this case I have to use ! RKS B3LYP 6-311G OPT RIJONX SV/C XYZFile %plots Format Cube MO("abc.cube",4,0) ; end this means orca will generate a cube file (abc.cube) only for the MO 4 of the closed shell RKS operator? Lets say 37th orbital is HOMO for my system, and if I am interested from HOMO-4 to LUMO+4 then I have to mention the following : MO("33.cube",33,0) ; MO("34.cube",34,0) ; ...................... MO("42.cube",42,0) ; is it rite? Simply, for each and every orbital of my interest I have to provide an option (MO keyword) in the orca input file; rite? Ofcourse, orca_2mkl utility programme works well to plot the MOs using Molekel, but still i wanted to try this one. Any explanation will be appreciated. Thank you very much in advance. Regards, Raji. From owner-chemistry@ccl.net Fri Mar 3 01:15:00 2006 From: "Dr. Seth Olsen s.olsen1**uq.edu.au" To: CCL Subject: CCL: Excellent computational chemistry group webpages Message-Id: <-31093-060303011259-12866-xTeMGp0H9eWFdIyesIlFaw##server.ccl.net> X-Original-From: "Dr. Seth Olsen" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 03 Mar 2006 16:12:50 +1000 MIME-Version: 1.0 Sent to CCL by: "Dr. Seth Olsen" [s.olsen1\a/uq.edu.au] Hi CCL'ers, After downloading yet another good lecture notes page on the Sherrill group webpage (http://vergil.chemistry.gatech.edu), it occurred to me what a nice resource it is to have members of the comp. chem. community which provide such nice webpages with useful content for the whole community. I thought it might be good to start a thread here asking for people to throw in the addresses of their favorite websites for computational chemistry research groups. Hopefully, these websites will have, for example, free lecture notes, downloadable publications in PDF, and numerous links to other useful CC sites. I'll start it off with two: The Sherrill group site and the Martinez Group site. The latter is only partially a plug (my PhD lab) - its also got a lot of good info & free pubs & notes. Sherrill Group: http://vergil.chemistry.gatech.edu Martinez Group: http://mtzweb.scs.uiuc.edu I encourage everyone to pipe up with their favorites, so that we can all benefit. This might have been done before, in which let me know and I'll go sort through the archives. Is the search engine working now? Cheers, Seth -- ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1(0)uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms From owner-chemistry@ccl.net Fri Mar 3 03:27:00 2006 From: "Raji Raji raji^_^anal.chem.tohoku.ac.jp" To: CCL Subject: CCL: ORCA Message-Id: <-31094-060303032550-17254-8bfiS8nOZVYQF0AvdkhSyA||server.ccl.net> X-Original-From: "Raji Raji" Date: Fri, 3 Mar 2006 03:25:46 -0500 Sent to CCL by: "Raji Raji" [raji=anal.chem.tohoku.ac.jp] Dear CCL Members, Few hours ago I have posted a message regarding my doubts about ORCA calculations. I have received such a nice explanations from Dr. Frank (ORCA developing team). Thank you very much Dr. Frank and ORCA developing team. Here I would like to summarise those results for your future reference. In addition with orca_plot utility programme, I found that the orca_2mkl utility programme works well to plot the MOs using Molekel. Regards, Raji. Dear Raj, 1) For TDDFT/TDA calculations with B3LYP/6-311G, in the COSMO part, I have to mention both solvent dielectric constant and refractive index? or just dielectric constant is enough? .. you have to provide the refractive index as well in CIS/TD-DFT; this is for the program to figure out the "fast" and "slow" solvent response. Its given in the manual that the refractive index is used only for CIS or MRCI modules. .. that is true; the MRCI module uses a somewhat approximate perturbation theory which needs more testing before i generally recommend it. Since in ORCA, CIS keyword is applicable for both CIS and TDDFT calculations, I got confused. So the refractive index is also necessary for TDDFT/TDA with hybrid functionals? By the way I am using RI approximation too. .. both CIS and TD-DFT/TDA pass through the same code. If you have a DFT SCF calculation you will get TD-DFT/TDA, if you have a Hartree-Fock ground state SCF calculation you'll get a CIS excited state calculation. So, no worries necessary - the program decides for you! 2) When I use RI approximation (RIJONX for the same hybrid function and basis set), it will only be applied to the Coulomb term; .. this is a sensible question. In RIJONX mode with hybrid functionals the RI approximation is only applied to the Coulomb term during the SCF iterations (this still saves a lot of time for larger molecules since the exchange is nearly linear scaling with molecule size in contrast to the Coulomb term). In the TD-DFT calculations RI is applied to both - the Coulomb and the exchange term. In our experience, the errors that you obtain in TD-DFT via the RI approximation are truly minimal even with the standard Coulomb fitting basis sets (for standard basis sets SV/C is also ok; it is only when you have additional diffuse functions in the basis set that you really should also augment the fitting basis). Technically speaking one should probably have different aux sets for the Coulomb and exchange parts but numerical evidence did so far not support that this is necessary. You can also use automatically generated auxiliary basis sets (AutoAux keyword), which are a little larger than the incredibly nice standard fit sets of the Ahlrichs group but AutoAux generates "general purpose" fit sets. Of course, as always in science - if you are in doubt of your results, you have to test the accuracy of the calculations by running a representative calculation with and without RI! 3) When I do population analysis, I want to analyse the results using molekel. so in this case I have to use ! RKS B3LYP 6-311G OPT RIJONX SV/C XYZFile %plots Format Cube MO("abc.cube",4,0) ; end this means orca will generate a cube file (abc.cube) only for the MO 4 of the closed shell RKS operator? Lets say 37th orbital is HOMO for my system, and if I am interested from HOMO-4 to LUMO+4 then I have to mention the following : MO("33.cube",33,0) ; MO("34.cube",34,0) ; ...................... MO("42.cube",42,0) ; .. yes this is all correct if you want to obtain these files via the ORCA input. Of course you can use the simple way of generating the cube files interactively by running orca_plot MyJob.gbw -i then you will get a "stone age" menu which lets you choose the ouput format, number of grid points and MOs to plot. This is how i usually do it and once you are familiar with orca_plot it is a really fast way from a calculation to a pretty picture. Hope that helps, have fun with ORCA! Frank From owner-chemistry@ccl.net Fri Mar 3 04:02:01 2006 From: "Frank Neese neese^mpi-muelheim.mpg.de" To: CCL Subject: CCL: ORCA - Solvation, RI approx. and Population Message-Id: <-31095-060303033728-24495-j4/kCW3ZZPy7I9aAJqu87w(~)server.ccl.net> X-Original-From: Frank Neese Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Fri, 03 Mar 2006 08:42:57 +0100 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese-$-mpi-muelheim.mpg.de] Dear Raj, 1) For TDDFT/TDA calculations with B3LYP/6-311G, in the COSMO part, I have to mention both solvent dielectric constant and refractive index? or just dielectric constant is enough? ... you have to provide the refractive index as well in CIS/TD-DFT; this is for the program to figure out the "fast" and "slow" solvent response. Its given in the manual that the refractive index is used only for CIS or MRCI modules. ... that is true; the MRCI module uses a somewhat approximate perturbation theory which needs more testing before i generally recommend it. Since in ORCA, CIS keyword is applicable for both CIS and TDDFT calculations, I got confused. So the refractive index is also necessary for TDDFT/TDA with hybrid functionals? By the way I am using RI approximation too. ... both CIS and TD-DFT/TDA pass through the same code. If you have a DFT SCF calculation you will get TD-DFT/TDA, if you have a Hartree-Fock ground state SCF calculation you'll get a CIS excited state calculation. So, no worries necessary - the program decides for you! 2) When I use RI approximation (RIJONX for the same hybrid function and basis set), it will only be applied to the Coulomb term; ... this is a sensible question. In RIJONX mode with hybrid functionals the RI approximation is only applied to the Coulomb term during the SCF iterations (this still saves a lot of time for larger molecules since the exchange is nearly linear scaling with molecule size in contrast to the Coulomb term). In the TD-DFT calculations RI is applied to both - the Coulomb and the exchange term. In our experience, the errors that you obtain in TD-DFT via the RI approximation are truly minimal even with the standard Coulomb fitting basis sets (for standard basis sets SV/C is also ok; it is only when you have additional diffuse functions in the basis set that you really should also augment the fitting basis). Technically speaking one should probably have different aux sets for the Coulomb and exchange parts but numerical evidence did so far not support that this is necessary. You can also use automatically generated auxiliary basis sets (AutoAux keyword), which are a little larger than the incredibly nice standard fit sets of the Ahlrichs group but AutoAux generates "general purpose" fit sets. Of course, as always in science - if you are in doubt of your results, you have to test the accuracy of the calculations by running a representative calculation with and without RI! 3) When I do population analysis, I want to analyse the results using molekel. so in this case I have to use ! RKS B3LYP 6-311G OPT RIJONX SV/C XYZFile %plots Format Cube MO("abc.cube",4,0) ; end this means orca will generate a cube file (abc.cube) only for the MO 4 of the closed shell RKS operator? Lets say 37th orbital is HOMO for my system, and if I am interested from HOMO-4 to LUMO+4 then I have to mention the following : MO("33.cube",33,0) ; MO("34.cube",34,0) ; ...................... MO("42.cube",42,0) ; ... yes this is all correct if you want to obtain these files via the ORCA input. Of course you can use the simple way of generating the cube files interactively by running orca_plot MyJob.gbw -i then you will get a "stone age" menu which lets you choose the ouput format, number of grid points and MOs to plot. This is how i usually do it and once you are familiar with orca_plot it is a really fast way from a calculation to a pretty picture. Hope that helps, have fun with ORCA! Frank From owner-chemistry@ccl.net Fri Mar 3 05:55:01 2006 From: "John Simmie john.simmie]_[nuigalway.ie" To: CCL Subject: CCL: Thermodynamic reversibility criterion Message-Id: <-31096-060303050902-5599-CJOfSnL+CjkoOhOZjKowKg*_*server.ccl.net> X-Original-From: John Simmie Content-type: multipart/alternative; boundary="Boundary_(ID_sauQiCYe11HXHeutKYUT0w)" Date: Fri, 03 Mar 2006 08:48:00 +0000 MIME-version: 1.0 Sent to CCL by: John Simmie [john.simmie|nuigalway.ie] --Boundary_(ID_sauQiCYe11HXHeutKYUT0w) Content-type: text/plain; charset=us-ascii; format=flowed Gonzalo: All elementary reactions are reversible no matter what the entropy or enthalpy changes amount to. according to the principle of microscopic reversibility ie Nature does not discriminate between reactants and products ... the paths traced out from reactant ==> product are identical to those from product ==> reactant The connection between kinetics & thermodynamics is given by k(forward) / k(reverse) = K where k's are rate constants and K is equilibrium constant .... from this you can relate k(reverse) to k(forward) and Gibbs free energy or enthalpy & entropy Trust this clarifies the position, John At 02:58 03/03/2006, you wrote: >Sent to CCL by: "Dr. Seth Olsen" [s.olsen1**uq.edu.au] > >Hi Gonzalo, > >A reaction is reversible if the entropy change is zero. If the >activation barriers are different for the forward and reverse reactions >then the forward and reverse rates will be different, but this is not >the same as thermodynamic reversibility. I recommend Dill & Blomberg's >'Molecular Driving Forces' for further info, though most chemical >thermodynamics texts will do. > >Cheers, > >Seth > > > >Gonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote: > > >Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez a dq.unirioja.es] > >Dear colleagues, > > > >Could anyone shed some light into the reversivility of chemical > processes attending to thermodynamic criteria, please?. Everybody > tend to say that a reaction is reversible when the activation > barrier from the products to a TS is lower or "comparable" with the > one which goes from the reactants to the same TS. My question is if > there is a Gibbs energy value (or range) that could make us to > discriminate between reversible and irreversible processes. > > > >Thank you all> > > > > > > > > > > >-- >ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > >Dr Seth Olsen, PhD >Postdoctoral Fellow, Biomolecular Modeling Group >Centre for Computational Molecular Science >Chemistry Building, >The University of Queensland >Qld 4072, Brisbane, Australia > >tel (617) 33653732 >fax (617) 33654623 >email: s.olsen1{:}uq.edu.au >Web: www.ccms.uq.edu.au > >ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsProfessor John M. Simmie Chemistry Department & Environmental Change Institute National University of Ireland, Galway::Ireland Phone: +353-91-492451::Fax: +353-91-525700 Mobile: +353-86-805-9948 Website: www.nuigalway.ie/chem/combust.htm --Boundary_(ID_sauQiCYe11HXHeutKYUT0w) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE =0D=0A=0D=0AGonzalo:
=0D=0AAll elementary reactions ar= e reversible no matter what the entropy or=0D=0Aenthalpy changes amou= nt to.
=0D=0Aaccording  to the principle of microscopic rever= sibility

=0D=0Aie Nature does not discriminate between reactan= ts and products ... the=0D=0Apaths traced out from
=0D=0Areactant = =3D=3D> product are identical to those from product =3D=3D>= =0D=0Areactant

=0D=0AThe connection between kinetics & the= rmodynamics is given by=0D=0Ak(forward) / k(reverse) =3D K
=0D= =0Awhere k's are rate constants and K is equilibrium constant .... fr= om this=0D=0Ayou can relate
=0D=0Ak(reverse) to k(forward) and Gib= bs free energy or enthalpy &=0D=0Aentropy

=0D=0ATrust this= clarifies the position, John

=0D=0AAt 02:58 03/03/2006, you w= rote:
=0D=0A
Sent to= CCL by: "Dr. Seth=0D=0AOlsen" [s.olsen1**uq.edu.au]
=0D=0AHi Gonzalo,

=0D=0AA reaction is reversible if the entro= py change is zero.  If the=0D=0A
=0D=0Aactivation barriers ar= e different for the forward and reverse reactions=0D=0A
=0D=0Athen= the forward and reverse rates will be different, but this is not= =0D=0A
=0D=0Athe same as thermodynamic reversibility.  I reco= mmend Dill &=0D=0ABlomberg's
=0D=0A'Molecular Driving Forces'= for further info, though most chemical
=0D=0Athermodynamics text= s will do.

=0D=0ACheers,

=0D=0ASeth

=0D=0A
=0D=0AGonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote:<= br>
=0D=0A>Sent to CCL by: "Gonzalo Jimenez Oses" [go= nzalo.jimenez a=0D=0Adq.unirioja.es]
=0D=0A>Dear colleagues,=0D=0A>
=0D=0A>Could anyone shed some light into the revers= ivility of chemical=0D=0Aprocesses attending to thermodynamic criteri= a, please?. Everybody tend to=0D=0Asay that a reaction is reversible = when the activation barrier from the=0D=0Aproducts to a TS is lower o= r "comparable" with the one which=0D=0Agoes from the reacta= nts to the same TS. My question is if there is a=0D=0AGibbs energy va= lue (or range) that could make us to discriminate between=0D=0Arevers= ible and irreversible processes.
=0D=0A>
=0D=0A>Thank you= all>
=0D=0A>
=0D=0A>
=0D=0A> 
=0D=0A&g= t;

=0D=0A
=0D=0A--
=0D=0Accmsccmsccmsccmsccmsccmsccmscc= msccmsccmsccmsccmsccmsccmsccmsccms

=0D=0ADr Seth Olsen, PhD=0D=0APostdoctoral Fellow, Biomolecular Modeling Group
=0D=0ACent= re for Computational Molecular Science
=0D=0AChemistry Building,=0D=0AThe University of Queensland
=0D=0AQld 4072, Brisbane, Aus= tralia

=0D=0Atel (617) 33653732
=0D=0Afax (617) 33654623=0D=0Aemail: s.olsen1{:}uq.edu.au
=0D=0AWeb:=0D=0A=0D=0Awww.ccms.uq.edu.au

=0D=0Accmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsc= cmsccmsccms

=0D=0A

=0D=0A-=3D This is automatically add= ed to each message by the mailing script=0D=0A=3D-
=0D=0ATo recove= r the email address of the author of the message, please=0D=0Achange<= br>=0D=0Athe strange characters on the top line to the % sign. You ca= n also
=0D=0A=

=0D=0A
= =0D=0A     =0D=0A=0D=0Ahttp://www.= ccl.net/cgi-bin/ccl/send_ccl_message

=0D=0AE-mail to admin= istrators: CHEMISTRY-REQUEST%ccl.net or use
=0D=0A  &nbs= p;  =0D=0A=0D=0Ahttp://www.ccl.net/cgi-bin/ccl/se= nd_ccl_message

=0D=0A
=0D=0A&nbs= p;    =0D=0A=0D=0Ahttp://www.ccl.net/chemi= stry/sub_unsub.shtml

=0D=0ABefore posting, check wait time= at:=0D=0Ahttp://ww= w.ccl.net
=0D=0A
=0D=0AJob:=0D=0A=0D=0Ahttp://www.ccl.net/jobs
= =0D=0AConferences:=0D=0A=0D=0Ahttp://server.ccl.= net/chemistry/announcements/conferences/

=0D=0ASearch Mess= ages:=0D=0A=0D=0Ahttp://www.ccl.net/htdig (login: ccl, Password: search)
=0D=0A=0D=0A     =0D=0A=0D=0Ahttp://www.ccl.net/spammer= s.txt

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=0D=0A=0D=0A   &nbs= p;        =0D=0AProfessor Joh= n M. Simmie
=0D=0AChemistry Department & Environmental Change = Institute
=0D=0A   National University of Ireland, Galwa= y::Ireland
=0D=0A     Phone: +353-91-492451::F= ax: +353-91-525700
=0D=0A       = ;     =0D=0AMobile: +353-86-805-9948
= =0D=0A     Website:=0D=0A=0D=0Awww.nuigalway.i= e/chem/combust.htm =0D=0A=0D=0A= --Boundary_(ID_sauQiCYe11HXHeutKYUT0w)-- From owner-chemistry@ccl.net Fri Mar 3 06:30:01 2006 From: "Tamas E. Gunda tgunda2005,+,puma.unideb.hu" To: CCL Subject: CCL: software patents Message-Id: <-31097-060303040519-6779-sF/Z4oayBIqknzUNeK1vzg%x%server.ccl.net> X-Original-From: "Tamas E. Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-2" Date: Fri, 3 Mar 2006 08:59:55 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas E. Gunda" [tgunda2005{:}puma.unideb.hu] I'm a simple chemist at a university and with only few years of industrial practice. I'm not a patent lawyer or specialist. However, many chemical patents were in my hand in order to try to reproduce a procedure or only to get ideas, to learn what others did and how. I quickly learned that a considerable part of the patents is unreliable or rubbish. Real and good procedures can be obtained only from the know-hows and they must be bought from the developers for money. Experts used to say that the aim of a patent is often only to mislead others. What is the situation in the case of software patents? Tamas E. Gunda tgunda2005---puma.unideb.hu From owner-chemistry@ccl.net Fri Mar 3 07:23:00 2006 From: "Mariusz Radon mariusz.radon()gmail.com" To: CCL Subject: CCL: Thermodynamic reversibility criterion Message-Id: <-31098-060303055916-13103-/XpCIFhiSbd64I78zd8lHw++server.ccl.net> X-Original-From: "Mariusz Radon" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 3 Mar 2006 11:59:03 +0100 MIME-Version: 1.0 Sent to CCL by: "Mariusz Radon" [mariusz.radon++gmail.com] Hi, In general case TdS-DQ = 0 (where DQ is a differential form of heat) is a condition for thermodynamic equilibrium (therm. reversibility). This equation is a basis for deriving well known expression under different conditions, such as dG=0 when p,T=const. It is important that thermodynamic reversibitly is not a feature of reaction (i.e. is determined not only by reagents, but depend also on conditions and reaction progress). So, I think you asked about chemical reversibility. If we go into thermodynamics considerations we ussually assume state of equilibrium (th. reversibility) has been reached. Restricting to isobaric and isotermic processes and taking into account the equation dG=0, where G depends on concentration of reagents, one may derive Guldberg-Waage law, with chemical equilibrium constant, K. In this sense each chemical process *is* reversible (because both "subst->prod" like "prod->subst" reactions are taking part), but if K is very huge we sometimes call it "irreversible". This means that in the state of equilibrium the concentration of products is much bigger than substrates and the velocity of forming products exceed the velocity of re-forming substrates. Because in mentioned conditions (p,T=const): K=\exp(-\Delta G^0 / RT) one may conclude that reaction is practically irreversible (in chem. sense!) when \Delta G^0 << 0. Here \Delta G^0 means "standard change of Gibb's free enalphy", which is the difference between the sum of G (per mol) for products and substrates (not dG in thermodynamics!). In some practical cases G \approx E + const, thus the criterium given by Gonzalo holds. But of course sometimes changes of entrophy and volume comes into play -- than one should employ full Gibb's free entalphy. Take care, Mariusz On 3/3/06, Dr. Seth Olsen s.olsen1%uq.edu.au wrote: > Sent to CCL by: "Dr. Seth Olsen" [s.olsen1**uq.edu.au] > > Hi Gonzalo, > > A reaction is reversible if the entropy change is zero. If the > activation barriers are different for the forward and reverse reactions > then the forward and reverse rates will be different, but this is not > the same as thermodynamic reversibility. I recommend Dill & Blomberg's > 'Molecular Driving Forces' for further info, though most chemical > thermodynamics texts will do. > > Cheers, > > Seth > > > > Gonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote: > > >Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez a dq.unirioja.es] > >Dear colleagues, > > > >Could anyone shed some light into the reversivility of chemical processes attending to thermodynamic criteria, please?. Everybody tend to say that a reaction is reversible when the activation barrier from the products to a TS is lower or "comparable" with the one which goes from the reactants to the same TS. My question is if there is a Gibbs energy value (or range) that could make us to discriminate between reversible and irreversible processes. > > > >Thank you all> > > > > > > > > > > > -- > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > > Dr Seth Olsen, PhD > Postdoctoral Fellow, Biomolecular Modeling Group > Centre for Computational Molecular Science > Chemistry Building, > The University of Queensland > Qld 4072, Brisbane, Australia > > tel (617) 33653732 > fax (617) 33654623 > email: s.olsen1{:}uq.edu.au > Web: www.ccms.uq.edu.au > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms> > > > -- Mariusz Rado\'n e-mail: mradon/at/chemia.uj.edu.pl e-mail & im: mariusz.radon/at/gmail.com From owner-chemistry@ccl.net Fri Mar 3 07:57:00 2006 From: "Thomas H Dr Pierce TPierce#,#rohmhaas.com" To: CCL Subject: CCL: Thermodynamic reversibility criterion Message-Id: <-31099-060303075326-16296-gu7g1hgt+uOKLCJ49kwThg(!)server.ccl.net> X-Original-From: Thomas H Dr Pierce Content-Type: multipart/alternative; boundary="=_alternative 0046CCFC85257126_=" Date: Fri, 3 Mar 2006 07:53:20 -0500 MIME-Version: 1.0 Sent to CCL by: Thomas H Dr Pierce [TPierce++rohmhaas.com] This is a multipart message in MIME format. --=_alternative 0046CCFC85257126_= Content-Type: text/plain; charset="US-ASCII" Gonzalo, Another generalization is that all physical processes are irreversible. The reason we do not have any perpetual motion systems is that a reaction loses some entropy or heat. If we define the "system" to allow for modest energy back into the system, we get reactions that behave as if they are reversible. But they consume energy so the are not strictly thermodynamically reversible. I consider the principle of microscopic reversibility to mean that a path in either direction is possible given the energy input or output needed. Water breaking into ions and back comes to mind as a room temperature event. The rate of forward to backward reactions assumes an energy source or bath. High transition barriers can be overcome if there is sufficient energy. Making Diamond from carbon and of course burning diamond is an example of this at high barriers requiring significant energy. It always seems like it is the definition of the "system" that carries the answer. ------ Sincerely, Tom Pierce "John Simmie john.simmie]_[nuigalway.ie" Sent by: owner-chemistry[#]ccl.net 03/03/2006 06:13 AM Please respond to "CCL Subscribers" To "Pierce, Tom " cc Subject CCL: Thermodynamic reversibility criterion Sent to CCL by: John Simmie [john.simmie|nuigalway.ie] --Boundary_(ID_sauQiCYe11HXHeutKYUT0w) Content-type: text/plain; charset=us-ascii; format=flowed Gonzalo: All elementary reactions are reversible no matter what the entropy or enthalpy changes amount to. according to the principle of microscopic reversibility ie Nature does not discriminate between reactants and products ... the paths traced out from reactant ==> product are identical to those from product ==> reactant The connection between kinetics & thermodynamics is given by k(forward) / k(reverse) = K where k's are rate constants and K is equilibrium constant .... from this you can relate k(reverse) to k(forward) and Gibbs free energy or enthalpy & entropy Trust this clarifies the position, John At 02:58 03/03/2006, you wrote: >Sent to CCL by: "Dr. Seth Olsen" [s.olsen1**uq.edu.au] > >Hi Gonzalo, > >A reaction is reversible if the entropy change is zero. If the >activation barriers are different for the forward and reverse reactions >then the forward and reverse rates will be different, but this is not >the same as thermodynamic reversibility. I recommend Dill & Blomberg's >'Molecular Driving Forces' for further info, though most chemical >thermodynamics texts will do. > >Cheers, > >Seth > > > >Gonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote: > > >Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez a dq.unirioja.es] > >Dear colleagues, > > > >Could anyone shed some light into the reversivility of chemical > processes attending to thermodynamic criteria, please?. Everybody > tend to say that a reaction is reversible when the activation > barrier from the products to a TS is lower or "comparable" with the > one which goes from the reactants to the same TS. My question is if > there is a Gibbs energy value (or range) that could make us to > discriminate between reversible and irreversible processes. > > > >Thank you all> > > > > > > > > > > >-- >ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > >Dr Seth Olsen, PhD >Postdoctoral Fellow, Biomolecular Modeling Group >Centre for Computational Molecular Science >Chemistry Building, >The University of Queensland >Qld 4072, Brisbane, Australia > >tel (617) 33653732 >fax (617) 33654623 >email: s.olsen1{:}uq.edu.au >Web: www.ccms.uq.edu.au > >ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsProfessor John M. Simmie Chemistry Department & Environmental Change Institute National University of Ireland, Galway::Ireland Phone: +353-91-492451::Fax: +353-91-525700 Mobile: +353-86-805-9948 Website: www.nuigalway.ie/chem/combust.htm --Boundary_(ID_sauQiCYe11HXHeutKYUT0w) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE =0D=0A=0D=0AGonzalo:
=0D=0AAll elementary reactions ar= e reversible no matter what the entropy or=0D=0Aenthalpy changes amou= nt to.
=0D=0Aaccording  to the principle of microscopic rever= sibility

=0D=0Aie Nature does not discriminate between reactan= ts and products ... the=0D=0Apaths traced out from
=0D=0Areactant = =3D=3D> product are identical to those from product =3D=3D>= =0D=0Areactant

=0D=0AThe connection between kinetics & the= rmodynamics is given by=0D=0Ak(forward) / k(reverse) =3D K
=0D= =0Awhere k's are rate constants and K is equilibrium constant .... fr= om this=0D=0Ayou can relate
=0D=0Ak(reverse) to k(forward) and Gib= bs free energy or enthalpy &=0D=0Aentropy

=0D=0ATrust this= clarifies the position, John

=0D=0AAt 02:58 03/03/2006, you w= rote:
=0D=0A

Sent to= CCL by: "Dr. Seth=0D=0AOlsen" [s.olsen1**uq.edu.au]
=0D=0AHi Gonzalo,

=0D=0AA reaction is reversible if the entro= py change is zero.  If the=0D=0A
=0D=0Aactivation barriers ar= e different for the forward and reverse reactions=0D=0A
=0D=0Athen= the forward and reverse rates will be different, but this is not= =0D=0A
=0D=0Athe same as thermodynamic reversibility.  I reco= mmend Dill &=0D=0ABlomberg's
=0D=0A'Molecular Driving Forces'= for further info, though most chemical
=0D=0Athermodynamics text= s will do.

=0D=0ACheers,

=0D=0ASeth

=0D=0A
=0D=0AGonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote:<= br>
=0D=0A>Sent to CCL by: "Gonzalo Jimenez Oses" [go= nzalo.jimenez a=0D=0Adq.unirioja.es]
=0D=0A>Dear colleagues,=0D=0A>
=0D=0A>Could anyone shed some light into the revers= ivility of chemical=0D=0Aprocesses attending to thermodynamic criteri= a, please?. Everybody tend to=0D=0Asay that a reaction is reversible = when the activation barrier from the=0D=0Aproducts to a TS is lower o= r "comparable" with the one which=0D=0Agoes from the reacta= nts to the same TS. My question is if there is a=0D=0AGibbs energy va= lue (or range) that could make us to discriminate between=0D=0Arevers= ible and irreversible processes.
=0D=0A>
=0D=0A>Thank you= all>
=0D=0A>
=0D=0A>
=0D=0A> 
=0D=0A&g= t;

=0D=0A
=0D=0A--
=0D=0Accmsccmsccmsccmsccmsccmsccmscc= msccmsccmsccmsccmsccmsccmsccmsccms

=0D=0ADr Seth Olsen, PhD=0D=0APostdoctoral Fellow, Biomolecular Modeling Group
=0D=0ACent= re for Computational Molecular Science
=0D=0AChemistry Building,=0D=0AThe University of Queensland
=0D=0AQld 4072, Brisbane, Aus= tralia

=0D=0Atel (617) 33653732
=0D=0Afax (617) 33654623=0D=0Aemail: s.olsen1{:}uq.edu.au
=0D=0AWeb:=0D=0A=0D=0Awww.ccms.uq.edu.au

=0D=0Accmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsc= cmsccmsccms

=0D=0A

=0D=0A-=3D This is automatically add= ed to each message by the mailing script=0D=0A=3D-
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=0D=0A=0D=0A   &nbs= p;        =0D=0AProfessor Joh= n M. Simmie
=0D=0AChemistry Department & Environmental Change = Institute
=0D=0A   National University of Ireland, Galwa= y::Ireland
=0D=0A     Phone: +353-91-492451::F= ax: +353-91-525700
=0D=0A       = ;     =0D=0AMobile: +353-86-805-9948
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Gonzalo,

Another generalization is that all physical processes are irreversible. The reason we do not have any perpetual motion systems is that  a reaction loses some entropy or heat.  If we define the "system" to allow for modest energy back into the system, we get reactions that behave as if they are reversible. But they consume energy so the are not strictly thermodynamically reversible.

I consider the principle of microscopic reversibility to mean that a path in either direction is possible given the energy input or output needed.  Water breaking into ions and back comes to mind as a room temperature event. The rate of forward to backward reactions assumes an energy source or bath. High transition barriers can be overcome if there is sufficient energy.  Making Diamond from carbon and of course burning diamond is an example of this at high barriers requiring significant energy.

It always seems like it is the definition of the "system" that carries the answer.
------
Sincerely,

  Tom Pierce
 


"John Simmie john.simmie]_[nuigalway.ie" <owner-chemistry[#]ccl.net>
Sent by: owner-chemistry[#]ccl.net

03/03/2006 06:13 AM
Please respond to
"CCL Subscribers" <chemistry[#]ccl.net>
To
"Pierce, Tom " <tpierce[#]rohmhaas.com>
cc
Subject
CCL: Thermodynamic reversibility criterion





Sent to CCL by: John Simmie [john.simmie|nuigalway.ie]

--Boundary_(ID_sauQiCYe11HXHeutKYUT0w)
Content-type: text/plain; charset=us-ascii; format=flowed

Gonzalo:
All elementary reactions are reversible no matter what the entropy or
enthalpy changes amount to.
according  to the principle of microscopic reversibility

ie Nature does not discriminate between reactants and products ...
the paths traced out from
reactant ==> product are identical to those from product ==> reactant

The connection between kinetics & thermodynamics is given by
k(forward) / k(reverse) = K
where k's are rate constants and K is equilibrium constant .... from
this you can relate
k(reverse) to k(forward) and Gibbs free energy or enthalpy & entropy

Trust this clarifies the position, John

At 02:58 03/03/2006, you wrote:
>Sent to CCL by: "Dr. Seth Olsen" [s.olsen1**uq.edu.au]
>
>Hi Gonzalo,
>
>A reaction is reversible if the entropy change is zero.  If the
>activation barriers are different for the forward and reverse reactions
>then the forward and reverse rates will be different, but this is not
>the same as thermodynamic reversibility.  I recommend Dill & Blomberg's
>'Molecular Driving Forces' for further info, though most chemical
>thermodynamics texts will do.
>
>Cheers,
>
>Seth
>
>
>
>Gonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote:
>
> >Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez a dq.unirioja.es]
> >Dear colleagues,
> >
> >Could anyone shed some light into the reversivility of chemical
> processes attending to thermodynamic criteria, please?. Everybody
> tend to say that a reaction is reversible when the activation
> barrier from the products to a TS is lower or "comparable" with the
> one which goes from the reactants to the same TS. My question is if
> there is a Gibbs energy value (or range) that could make us to
> discriminate between reversible and irreversible processes.
> >
> >Thank you all>
> >
> >
> >
> >
>
>
>--
>ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
>
>Dr Seth Olsen, PhD
>Postdoctoral Fellow, Biomolecular Modeling Group
>Centre for Computational Molecular Science
>Chemistry Building,
>The University of Queensland
>Qld 4072, Brisbane, Australia
>
>tel (617) 33653732
>fax (617) 33654623
>email: s.olsen1{:}uq.edu.au
>Web: www.ccms.uq.edu.au
>
>ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsProfessor John M. Simmie
Chemistry Department & Environmental Change Institute
   National University of Ireland, Galway::Ireland
     Phone: +353-91-492451::Fax: +353-91-525700
             Mobile: +353-86-805-9948
     Website: www.nuigalway.ie/chem/combust.htm  

--Boundary_(ID_sauQiCYe11HXHeutKYUT0w)
Content-type: text/html; charset=iso-8859-1
Content-transfer-encoding: QUOTED-PRINTABLE

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>=0D=0AHi Gonzalo,<br><br>=0D=0AA reaction is reversible if the entro=
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r>=0D=0AGonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote:<=
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nzalo.jimenez a=0D=0Adq.unirioja.es]<br>=0D=0A&gt;Dear colleagues,<br=
>=0D=0A&gt;<br>=0D=0A&gt;Could anyone shed some light into the revers=
ivility of chemical=0D=0Aprocesses attending to thermodynamic criteri=
a, please?. Everybody tend to=0D=0Asay that a reaction is reversible =
when the activation barrier from the=0D=0Aproducts to a TS is lower o=
r &quot;comparable&quot; with the one which=0D=0Agoes from the reacta=
nts to the same TS. My question is if there is a=0D=0AGibbs energy va=
lue (or range) that could make us to discriminate between=0D=0Arevers=
ible and irreversible processes.<br>=0D=0A&gt;<br>=0D=0A&gt;Thank you=
all&gt;<br>=0D=0A&gt;<br>=0D=0A&gt;<br>=0D=0A&gt;&nbsp; <br>=0D=0A&g=
t;<br><br>=0D=0A<br>=0D=0A-- <br>=0D=0Accmsccmsccmsccmsccmsccmsccmscc=
msccmsccmsccmsccmsccmsccmsccmsccms<br><br>=0D=0ADr Seth Olsen, PhD<br=
>=0D=0APostdoctoral Fellow, Biomolecular Modeling Group<br>=0D=0ACent=
re for Computational Molecular Science<br>=0D=0AChemistry Building,<b=
r>=0D=0AThe University of Queensland<br>=0D=0AQld 4072, Brisbane, Aus=
tralia<br><br>=0D=0Atel (617) 33653732<br>=0D=0Afax (617) 33654623<br=
>=0D=0Aemail: s.olsen1{:}uq.edu.au<br>=0D=0AWeb:=0D=0A<a href=3D"http=
://www.ccms.uq.edu.au" eudora=3D"autourl">=0D=0Awww.ccms.uq.edu.au</a=
> <br><br>=0D=0Accmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsc=
cmsccmsccms<br><br>=0D=0A<br><br>=0D=0A-=3D This is automatically add=
ed to each message by the mailing script=0D=0A=3D-<br>=0D=0ATo recove=
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--=_alternative 0046CCFC85257126_=-- From owner-chemistry@ccl.net Fri Mar 3 09:36:00 2006 From: "Lukasz Cwiklik cwiklik#gmail.com" To: CCL Subject: CCL: Thermodynamic reversibility criterion Message-Id: <-31100-060303042943-22401-tj+775NnS7/RvPy7U9iqNg_-_server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 3 Mar 2006 10:29:24 +0100 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik]^[gmail.com] On 3/3/06, Gonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote: > Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez a dq.unirioja.es] > Dear colleagues, > > Could anyone shed some light into the reversivility of chemical processes attending to thermodynamic criteria, please?. Everybody tend to say that a reaction is reversible when the activation barrier from the products to a TS is lower or "comparable" with the one which goes from the reactants to the same TS. My question is if there is a Gibbs energy value (or range) that could make us to discriminate between reversible and irreversible processes. Dear Gonzalo, In my opinion (I hope my remarks are not too general), the ratio of values of activation barriers on both sides of TS lets you to calculate the populations (or probabilities of observing, or cancentrations) of both reactatants and products (but only if your system is in thermodynamical equilibrium). So taking the Gibbs energy values you can calculate probabilities/rates of processes but you cannot _strictly_ discriminate between reversibility and irreversibility. One thing that is also important is the possibility of other processes in your system. If your reactants may form a product which then may undergo the reverse transition _or_ react along some other path, then you must be careful and, in your considerations of reversibility, you should take into account the barrier of this third process. Best regards, Lukasz -- Lukasz Cwiklik http://www.molecular.cz/~cwiklik From owner-chemistry@ccl.net Fri Mar 3 10:18:00 2006 From: "Ramon Crehuet rcsqtc=iiqab.csic.es" To: CCL Subject: CCL: Thermodynamic reversibility criterion Message-Id: <-31101-060303082237-3326-UZ1Z/jtBPM1r/gwErsUHWQ++server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 03 Mar 2006 13:30:37 +0100 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc++iiqab.csic.es] Hi all, Although microscopic reversibility always holds, even one-step reactions A-> B can, in practice, be irreversible. This is probably not what you see in textbooks, but an experimental chemist will probably tell you that they are irrevesible. This will happen when the products have other possible reaction paths, apart from that giving back the product A, specially if the rate of these processes is faster than the rate to give back the reactant A. So that, in a lab, once you have done A->B if you change the conditions to reverse the equilibrium, B will give C, D, E... instead of A. Cheers, Ramon John Simmie john.simmie]_[nuigalway.ie wrote: >Sent to CCL by: John Simmie [john.simmie|nuigalway.ie] > >--Boundary_(ID_sauQiCYe11HXHeutKYUT0w) >Content-type: text/plain; charset=us-ascii; format=flowed > >Gonzalo: >All elementary reactions are reversible no matter what the entropy or >enthalpy changes amount to. >according to the principle of microscopic reversibility > >ie Nature does not discriminate between reactants and products ... >the paths traced out from >reactant ==> product are identical to those from product ==> reactant > >The connection between kinetics & thermodynamics is given by >k(forward) / k(reverse) = K >where k's are rate constants and K is equilibrium constant .... from >this you can relate >k(reverse) to k(forward) and Gibbs free energy or enthalpy & entropy > >Trust this clarifies the position, John > >At 02:58 03/03/2006, you wrote: > > >>Sent to CCL by: "Dr. Seth Olsen" [s.olsen1**uq.edu.au] >> >>Hi Gonzalo, >> >>A reaction is reversible if the entropy change is zero. If the >>activation barriers are different for the forward and reverse reactions >>then the forward and reverse rates will be different, but this is not >>the same as thermodynamic reversibility. I recommend Dill & Blomberg's >>'Molecular Driving Forces' for further info, though most chemical >>thermodynamics texts will do. >> >>Cheers, >> >>Seth >> >> >> >>Gonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote: >> >> >> >>>Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez a dq.unirioja.es] >>>Dear colleagues, >>> >>>Could anyone shed some light into the reversivility of chemical >>> >>> >>processes attending to thermodynamic criteria, please?. Everybody >>tend to say that a reaction is reversible when the activation >>barrier from the products to a TS is lower or "comparable" with the >>one which goes from the reactants to the same TS. My question is if >>there is a Gibbs energy value (or range) that could make us to >>discriminate between reversible and irreversible processes. >> >> >>>Thank you all> >>> >>> >>> >>> >>> >>> >>-- >>ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms >> >>Dr Seth Olsen, PhD >>Postdoctoral Fellow, Biomolecular Modeling Group >>Centre for Computational Molecular Science >>Chemistry Building, >>The University of Queensland >>Qld 4072, Brisbane, Australia >> >>tel (617) 33653732 >>fax (617) 33654623 >>email: s.olsen1{:}uq.edu.au >>Web: www.ccms.uq.edu.au >> >>ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsProfessor John M. Simmie >> >> >Chemistry Department & Environmental Change Institute > National University of Ireland, Galway::Ireland > Phone: +353-91-492451::Fax: +353-91-525700 > Mobile: +353-86-805-9948 > Website: www.nuigalway.ie/chem/combust.htm > >--Boundary_(ID_sauQiCYe11HXHeutKYUT0w) >Content-type: text/html; charset=iso-8859-1 >Content-transfer-encoding: QUOTED-PRINTABLE > >=0D=0A=0D=0AGonzalo:
=0D=0AAll elementary reactions ar= >e reversible no matter what the entropy or=0D=0Aenthalpy changes amou= >nt to.
=0D=0Aaccording  to the principle of microscopic rever= >sibility

=0D=0Aie Nature does not discriminate between reactan= >ts and products ... the=0D=0Apaths traced out from
=0D=0Areactant = >=3D=3D> product are identical to those from product =3D=3D>= >=0D=0Areactant

=0D=0AThe connection between kinetics & the= >rmodynamics is given by=0D=0Ak(forward) / k(reverse) =3D K
=0D= >=0Awhere k's are rate constants and K is equilibrium constant .... fr= >om this=0D=0Ayou can relate
=0D=0Ak(reverse) to k(forward) and Gib= >bs free energy or enthalpy &=0D=0Aentropy

=0D=0ATrust this= > clarifies the position, John

=0D=0AAt 02:58 03/03/2006, you w= >rote:
=0D=0A

Sent to= > CCL by: "Dr. Seth=0D=0AOlsen" [s.olsen1**uq.edu.au]
> >>=0D=0AHi Gonzalo,

=0D=0AA reaction is reversible if the entro= >> >> >py change is zero.  If the=0D=0A
=0D=0Aactivation barriers ar= >e different for the forward and reverse reactions=0D=0A
=0D=0Athen= > the forward and reverse rates will be different, but this is not= >=0D=0A
=0D=0Athe same as thermodynamic reversibility.  I reco= >mmend Dill &=0D=0ABlomberg's
=0D=0A'Molecular Driving Forces'= > for further info, though most chemical
=0D=0Athermodynamics text= >s will do.

=0D=0ACheers,

=0D=0ASeth

=0D=0A
r>=0D=0AGonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es wrote:<= >br>
=0D=0A>Sent to CCL by: "Gonzalo Jimenez Oses" [go= >nzalo.jimenez a=0D=0Adq.unirioja.es]
=0D=0A>Dear colleagues, > >>=0D=0A>
=0D=0A>Could anyone shed some light into the revers= >> >> >ivility of chemical=0D=0Aprocesses attending to thermodynamic criteri= >a, please?. Everybody tend to=0D=0Asay that a reaction is reversible = >when the activation barrier from the=0D=0Aproducts to a TS is lower o= >r "comparable" with the one which=0D=0Agoes from the reacta= >nts to the same TS. My question is if there is a=0D=0AGibbs energy va= >lue (or range) that could make us to discriminate between=0D=0Arevers= >ible and irreversible processes.
=0D=0A>
=0D=0A>Thank you= > all>
=0D=0A>
=0D=0A>
=0D=0A> 
=0D=0A&g= >t;

=0D=0A
=0D=0A--
=0D=0Accmsccmsccmsccmsccmsccmsccmscc= >msccmsccmsccmsccmsccmsccmsccmsccms

=0D=0ADr Seth Olsen, PhD > >>=0D=0APostdoctoral Fellow, Biomolecular Modeling Group
=0D=0ACent= >> >> >re for Computational Molecular Science
=0D=0AChemistry Building,r>=0D=0AThe University of Queensland
=0D=0AQld 4072, Brisbane, Aus= >tralia

=0D=0Atel (617) 33653732
=0D=0Afax (617) 33654623 > >>=0D=0Aemail: s.olsen1{:}uq.edu.au
=0D=0AWeb:=0D=0A> >> >://www.ccms.uq.edu.au" eudora=3D"autourl">=0D=0Awww.ccms.uq.edu.au > >>

=0D=0Accmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsc= >> >> >cmsccmsccms

=0D=0A

=0D=0A-=3D This is automatically add= >ed to each message by the mailing script=0D=0A=3D-
=0D=0ATo recove= >r the email address of the author of the message, please=0D=0Achange<= >br>=0D=0Athe strange characters on the top line to the ]~[ sign. You ca= >n also
=0D=0A= >

=0D=0A
= >=0D=0A     =0D=0Aet/cgi-bin/ccl/send_ccl_message" eudora=3D"autourl">=0D=0Ahttp://www.= >ccl.net/cgi-bin/ccl/send_ccl_message

=0D=0AE-mail to admin= >istrators: CHEMISTRY-REQUEST]~[ccl.net or use
=0D=0A  &nbs= >p;  =0D=0Al_message" eudora=3D"autourl">=0D=0Ahttp://www.ccl.net/cgi-bin/ccl/se= >nd_ccl_message

=0D=0A
=0D=0A&nbs= >p;    =0D=0Ary/sub_unsub.shtml" eudora=3D"autourl">=0D=0Ahttp://www.ccl.net/chemi= >stry/sub_unsub.shtml

=0D=0ABefore posting, check wait time= > at:=0D=0Ahttp://ww= >w.ccl.net
=0D=0A
=0D=0AJob:=0D=0Anet/jobs" eudora=3D"autourl">=0D=0Ahttp://www.ccl.net/jobs
= >=0D=0AConferences:=0D=0Anouncements/conferences/" eudora=3D"autourl">=0D=0Ahttp://server.ccl.= >net/chemistry/announcements/conferences/

=0D=0ASearch Mess= >ages:=0D=0A > >>=0D=0Ahttp://www.ccl.net/htdig (login: ccl, Password: search)> >> >r>
=0D=0A > >>=0D=0A     =0D=0A> >> >net/spammers.txt" eudora=3D"autourl">=0D=0Ahttp://www.ccl.net/spammer= >s.txt

=0D=0ARTFI:=0D=0Astry/aboutccl/instructions/" eudora=3D"autourl">=0D=0Ahttp://www.ccl.= >net/chemistry/aboutccl/instructions/

=0D=0A-+-+-+-+-+-+-+-= >+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > >>=0D=0A

=0D=0A=0D=0A   &nbs= >> >> >p;        =0D=0AProfessor Joh= >n M. Simmie
=0D=0AChemistry Department & Environmental Change = >Institute
=0D=0A   National University of Ireland, Galwa= >y::Ireland
=0D=0A     Phone: +353-91-492451::F= >ax: +353-91-525700
=0D=0A       = >;     =0D=0AMobile: +353-86-805-9948
= >=0D=0A     Website:=0D=0Aigalway.ie/chem/combust.htm" eudora=3D"autourl">=0D=0Awww.nuigalway.i= >e/chem/combust.htm =0D=0A=0D=0A= > >--Boundary_(ID_sauQiCYe11HXHeutKYUT0w)--> > > > > > From owner-chemistry@ccl.net Fri Mar 3 14:29:00 2006 From: "Scott Brozell srb*osc.edu" To: CCL Subject: CCL: DOCK(grid) input files Message-Id: <-31102-060303142641-6451-54DO3jncuE1sLWiNpsv0mg:_:server.ccl.net> X-Original-From: Scott Brozell Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 3 Mar 2006 14:26:30 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Scott Brozell [srb%%osc.edu] Hi, Let me re-emphasize that the dock-fans list might reach more people that use DOCK: http://blur.compbio.ucsf.edu/pipermail/dock-fans/ Chimera is very popular. Another free software option is CADD tools: http://home.pchome.com.tw/team/gentamicin/mol/mol.htm See also http://dock.compbio.ucsf.edu/DOCK_Links/index.htm Scott On Thu, 2 Mar 2006, Elaine Meng meng~!~cgl.ucsf.edu wrote: > Hello, > Chimera includes a Dock Prep tool that does various tasks to prepare > a protein structure as input to DOCK's scoring grid calculation, > including adding charges. It also adds hydrogens, deletes alternate > locations, etc. > > This tool is in the most recent release of Chimera (February 2006) > and is described here: > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ > dockprep.html > > Chimera is free for noncommercial use and available for Windows, Mac, > and other platforms from: > http://www.cgl.ucsf.edu/chimera/ > > As for the other steps in using DOCK, I recommend looking at the > official DOCK web site > http://dock.compbio.ucsf.edu/ > > which includes some tutorials > http://dock.compbio.ucsf.edu/DOCK_5/index.htm > > and using the dock-fans mailing list or searching its archives > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng]*[cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > On Mar 2, 2006, at 6:00 AM, Senthil Kumar Natesan > senthilkumar_natesan .. bi.iiita.ac.in wrote: > >> Sent to CCL by: "Senthil Kumar >> Natesan" [senthilkumar_natesan_._bi.iiita.ac.in] >> >> Dear Colleagues, >> >> I am beginner in docking(using DOCK 5.3). Can anyone pls help me to >> add charges in mol2 file( I use openbabel to convert from pdb to >> mol2) without using SYBYL( I don't have access to SYBYL). >> >> I would be very grateful if someone could brief me all steps in >> docking database(ligands) or single ligand to a protein. >> >> Thanx in advance. From owner-chemistry@ccl.net Fri Mar 3 17:14:00 2006 From: "Alex Allardyce aa_._chemaxon.hu" To: CCL Subject: CCL: ChemAxon's 2006 UGM - June 7-8, Budapest : Second call for papers Message-Id: <-31103-060303171142-22770-chKzFRpKWzla0G5wkLXr3g : server.ccl.net> X-Original-From: "Alex Allardyce" Date: Fri, 3 Mar 2006 17:11:38 -0500 Sent to CCL by: "Alex Allardyce" [aa^chemaxon.hu] Excuse cross postings ChemAxons 2006 User Group Meeting will be held on Wednesday and Thursday, June 7th - 8th, 2006, once again at the Gellert Hotel, Budapest, Hungary. The meeting will include oral and poster presentations from ChemAxon users and developers and separate tracks on day 2, for both scientific and developer issues. We are inviting those interested in presenting at the meeting to submit abstracts for review. /The deadline for reciept of abstracts is March 17th. / We hope you can participate in what has proven to be a most exciting, relevant and enjoyable cheminformatics event. * To review the submission guidelines please visit http://www.chemaxon.com/forum/ftopic295.html . * To review the full presentations from the 2005 meeting archive please visit http://www.chemaxon.com/UGM/05/index.html * To visit the User Group Meeting index please visit: http://www.chemaxon.com/UGM/06/index.html If you have any questions please feel free to contact us. See you here. Alex Allardyce From owner-chemistry@ccl.net Fri Mar 3 17:49:01 2006 From: "Debasis Sengupta dxs]|[cfdrc.com" To: CCL Subject: CCL:G: Volume calculation in Gaussian Message-Id: <-31104-060303171833-25882-V3d4n1TmY2r55b/z+h+w1g..server.ccl.net> X-Original-From: Debasis Sengupta Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 03 Mar 2006 16:18:26 -0600 MIME-Version: 1.0 Sent to CCL by: Debasis Sengupta [dxs**cfdrc.com] Can anybody give me a reference of how Gaussian calculates volume using the keyword "volume"? Thanks Debasis From owner-chemistry@ccl.net Fri Mar 3 18:23:00 2006 From: "Judith Bandy jbandy ~ inforsense.com" To: CCL Subject: CCL: FIRST ANNOUNCEMENT: InforSense Users Conference, April 6-7, Boston, US Message-Id: <-31105-060303165138-16291-/sJF2B0kYRkqBwnBe+4mmQ(a)server.ccl.net> X-Original-From: "Judith Bandy" Date: Fri, 3 Mar 2006 16:51:34 -0500 Sent to CCL by: "Judith Bandy" [jbandy+*+inforsense.com] InforSense Users Conference, April 6-7 2006, Boston, USA We are very pleased to announce the first InforSense Users Conference, to be held on April 6-7 2006, in Boston, Massachusetts, USA. The Conference will provide you with the opportunity to learn how InforSense KDE is being used to enable business-critical decision making across a variety of industries. Contributions from Keynote Speakers, InforSense KDE users, Partners and InforSense Product Specialists will help you to maximize the value of InforSense technology in your organization. You will also have time to network with others in the InforSense community and the chance to provide your input into future integrative analytics product plans. This exciting and informative event will take place at the downtown Boston offices of Apple Computer in the Prudential Center, Boston. Attendance is free of charge. Please register today at (http://www.inforsense.com/user_group_meeting.html) to reserve your place and receive further information of this valuable event. For any other questions, please call Emma Cutting at +44 207 808 9524 or send email to information!A!inforsense.com. InforSense Ltd 459a Fulham Road Chelsea, London SW10 9UZ UK +44 207 808 9500 InforSense - North America 25 Moulton Street, Cambridge, MA 02138 USA +1 617 547 2500 www.inforsense.com 2006 InforSense Ltd. All rights reserved. InforSense, the InforSense logo and TextSense are registered trade-marks of InforSense Ltd. Open Discovery Workflow is a trademark of InforSense Ltd. All other brands or products names are trademarks of their respective holders From owner-chemistry@ccl.net Fri Mar 3 19:03:01 2006 From: "Veer Shanmugasundaram Veerabahu.Shanmugasundaram]^[pfizer.com" To: CCL Subject: CCL: Call for Papers - Estrogen Receptor Symposium Message-Id: <-31106-060303190143-30247-+oVlbHnDpQb91BYMCNvVHA[A]server.ccl.net> X-Original-From: "Veer Shanmugasundaram" Date: Fri, 3 Mar 2006 19:01:39 -0500 Sent to CCL by: "Veer Shanmugasundaram" [Veerabahu.Shanmugasundaram .. pfizer.com] Ligand-dependent activation and inactivation of transcription by nuclear hormone receptors are mediated by the recruitment of co-activators and/or co-repressors by the receptor. Receptor agonists promote co-activator binding while antagonists block co-activator binding or promote co-repressor binding thereby affecting transcriptional activity. At a molecular level, in the estrogen receptor, these mechanistic events have been explained to an extent by the solution of several estrogen receptor ligand binding domain (LBD) agonist and antagonist crystal structures. In the diethylstilbestrol (DES) agonist complex structure, the co-activator peptide binds to a hydrophobic groove on the surface of the LBD, which is promoted by a conformation of the LBD where the helix 12 is tucked over the binding pocket. In the 4-hydroxytamoxifen (OHT) antagonist structure, the side chain of OHT projects out of the ligand binding pocket, which promotes a conformation of the LBD that results in helix 12 blocking the coactivator recognition groove. However, ligands that are smaller in size (that do not have the OHT sidechain) also vary in functional activities as reported by results from several recent publications. Investigations into ER-subtype selective modulators (alpha vs beta) using structure-based methods have also been described in the literature. We plan to organize a mini-symposium that would bring together a diverse group of researchers and scientists at the 232nd National Fall ACS Meeting, San Francisco, CA, who have thought about and applied structure-based methods to the evaluation and development of selective and/or non-selective estrogen receptor modulators as well as selective and/or non-selective estrogen receptor subtype modulators. This symposium will be sponsored by the COMP division of the American Chemical Society. Symposium: Structure-Based Design & Development of Estrogen Receptor Modulators Venue : 232nd National Fall ACS Meeting, San Francisco, CA Dates : September 10th - 14th, 2006 Sponsored by : COMP Division Co-chairs : Veer Shanmugasundaram & Neil Raheja, Pfizer Global Research & Development, Ann Arbor, MI Please submit your abstracts for this symposium using OASYS http://oasys.acs.org/acs/232nm/comp/papers/index.cgi The deadline for submitting abstracts is April 25, 2006. Thank you, Veer. ---- Veer Shanmugasundaram, Ph.D Computer-Assisted Drug Discovery, Pfizer Global Research & Development, 2800 Plymouth Road, Ann Arbor, MI 48105. Tel:(734)622-7131 Fax:(734)622-2782 Email:Veerabahu.Shanmugasundaram[#]pfizer.com Neil Raheja, Ph.D Medicinal Chemistry, Pfizer Global Research & Development Ann Arbor, MI 48105 Tel: (734)622-2305 Fax:(734)622-3107 Email: Neil.Raheja[#]pfizer.com