From owner-chemistry@ccl.net Sat May 23 12:01:01 2009 From: "Richard Tia richtiagh%%gmail.com" To: CCL Subject: CCL: Downhill reactions Message-Id: <-39360-090523115732-12006-0mjyulirf3Zh8W4yEwMbzA/a\server.ccl.net> X-Original-From: "Richard Tia" Date: Sat, 23 May 2009 11:57:27 -0400 Sent to CCL by: "Richard Tia" [richtiagh^^gmail.com] Hi everyone, I want a clarification on something. In a strictly computational chemistry sense, what does it mean to say that a given reaction proceeds 'downhill'? and how different is that from a 'barrierless' reaction? Any examples? Thanks so much in advance for any help. Richard Tia Department of Chemistry KNUST, Kumasi GHANA From owner-chemistry@ccl.net Sat May 23 16:38:00 2009 From: "Stephen Bowlus chezbowlus]=[comcast.net" To: CCL Subject: CCL: Downhill reactions Message-Id: <-39361-090523154339-22591-XXYpgHY34NAHAtitNRpfkA]-[server.ccl.net> X-Original-From: Stephen Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Sat, 23 May 2009 12:09:05 -0700 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Stephen Bowlus [chezbowlus .. comcast.net] Our students are taught strictly to separate thermodynamics from kinetics. A "downhill" reaction for us is one with a negative change in enthalpy (exothermic) and/or free energy (endergonic). This says absolutely nothing about the rate of the reaction (chiefly the barrier height). AFAIK, experimentalists (me) and computational chemists (also me) share these ideas. -sb On May 23, 2009, at 8:57 AM, Richard Tia richtiagh%%gmail.com wrote: > > Sent to CCL by: "Richard Tia" [richtiagh^^gmail.com] > Hi everyone, > I want a clarification on something. In a strictly computational > chemistry sense, what does it mean to say that a given reaction > proceeds 'downhill'? and how different is that from a 'barrierless' > reaction? Any examples? > Thanks so much in advance for any help. > > Richard Tia > Department of Chemistry > KNUST, Kumasi > GHANA > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > From owner-chemistry@ccl.net Sat May 23 17:27:01 2009 From: "Kalju Kahn kalju_+_chem.ucsb.edu" To: CCL Subject: CCL: SOS - problem with Tinker pbsxyz routine Message-Id: <-39362-090523164132-28179-4tjI+jegi7Mpd9mm7q3Taw]-[server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 23 May 2009 13:40:53 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju**chem.ucsb.edu] Marek, > OK anyway, I am looking for some MM SW which is able to use mainly > Amber forcefields/Gaff to help me derive some missing Amber ff > parameters in case of "nonstandard" compounds like Si by fitting > MM relative energies, rotational profiles using QM ones. It seems > to me that Molden+Tinker could be a good candidate for this kind of > job, but if you know something better, please just let me know. I think you have some difficult time here with MOLDEN. It does support AMBER for proteins/nucleic acids, and AMBFOR/GAFF for general organics, but neither knows about silicon. In other words, you cannot assign Amber or GAFF atom types to Si-containing molecules. (Can do Tinker-MM3, though) If it is an organosilicon compound, it seems that you need to use Gaff, which is not supported by Tinker .... could use MOLDEN after defining Silicon and its parameters in the source code but the force field parameters are compiled into the program, making parameterization painful. If it is a silicon-containing amino acid ... something that Amber almost knows, then Tinker will be the tool of choice; the only time I would use MOLDEN is to prepare the initial structures where all atoms but silicon is correctly typed ... fool it by telling that you have a carbon there, then change it back to Si in the xyz file created before optimization. Best regards, Kalju ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Sat May 23 19:00:00 2009 From: "Marek Maly marek.maly]^[ujep.cz" To: CCL Subject: CCL: SOS - problem with Tinker pbsxyz routine Message-Id: <-39363-090523180900-25210-5ZVM6tUpweGubr5Svxneqw_-_server.ccl.net> X-Original-From: "Marek Maly" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=iso-8859-2 Date: Sun, 24 May 2009 00:08:55 +0200 MIME-Version: 1.0 Sent to CCL by: "Marek Maly" [marek.maly/a\ujep.cz] Hi Kalju, thanks a lot for your suggestions ! Forcefield parameters development for "nonstandard" compounds (like Si) is probably always a little "painful" work :)) For this moment I decided to use for MM part of job Amber/GAFF (using FRCMOD file to add/test new bond, angle, dihed and vdw parm.) and for QM part Gamess and as I see it will probably work good. Best, Marek Dne Sat, 23 May 2009 22:40:53 +0200 Kalju Kahn kalju_+_chem.ucsb.edu napsal/-a: > > Sent to CCL by: "Kalju Kahn" [kalju**chem.ucsb.edu] > Marek, > >> OK anyway, I am looking for some MM SW which is able to use mainly >> Amber forcefields/Gaff to help me derive some missing Amber ff >> parameters in case of "nonstandard" compounds like Si by fitting >> MM relative energies, rotational profiles using QM ones. It seems >> to me that Molden+Tinker could be a good candidate for this kind of >> job, but if you know something better, please just let me know. > > I think you have some difficult time here with MOLDEN. It does support > AMBER for proteins/nucleic acids, and AMBFOR/GAFF for general organics, > but neither knows about silicon. In other words, you cannot assign Amber > or GAFF atom types to Si-containing molecules. (Can do Tinker-MM3, > though) > > If it is an organosilicon compound, it seems that you need to use Gaff, > which is not supported by Tinker .... could use MOLDEN after defining > Silicon and its parameters in the source code but the force field > parameters are compiled into the program, making parameterization > painful. > > If it is a silicon-containing amino acid ... something that Amber almost > knows, then Tinker will be the tool of choice; the only time I would use > MOLDEN is to prepare the initial structures where all atoms but silicon > is > correctly typed ... fool it by telling that you have a carbon there, then > change it back to Si in the xyz file created before optimization. > > Best regards, > > Kalju > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kalju Kahn > Department of Chemistry and Biochemistry > UC Santa Barbara, CA 93106> > > > __________ Informace od NOD32 4051 (20090504) __________ > > Tato zprava byla proverena antivirovym systemem NOD32. > http://www.nod32.cz > > -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ From owner-chemistry@ccl.net Sat May 23 19:35:00 2009 From: "Stephen Bowlus chezbowlus]~[comcast.net" To: CCL Subject: CCL: Downhill reactions -- oops Message-Id: <-39364-090523192000-13533-4FHG/9XGMlaK78hTzvnunw-*-server.ccl.net> X-Original-From: Stephen Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Sat, 23 May 2009 16:19:19 -0700 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Stephen Bowlus [chezbowlus\a/comcast.net] > Of course, I meant EXergonic for a negative free energy change. > Yeesh! > > -sb > > >> Our students are taught strictly to separate thermodynamics from >> kinetics. A "downhill" reaction for us is one with a negative >> change in enthalpy (exothermic) and/or free energy (endergonic). >> This says absolutely nothing about the rate of the reaction >> (chiefly the barrier height). AFAIK, experimentalists (me) and >> computational chemists (also me) share these ideas.