From owner-chemistry@ccl.net Fri Apr 29 04:26:00 2011 From: "servaas servaas.michielssens**student.kuleuven.be" To: CCL Subject: CCL:G: implicit solvation Message-Id: <-44485-110429040837-22776-MsOiA3Obgl/yckXlheV42w^^^server.ccl.net> X-Original-From: servaas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Fri, 29 Apr 2011 10:08:07 +0200 Mime-Version: 1.0 Sent to CCL by: servaas [servaas.michielssens[*]student.kuleuven.be] According to the procedure described in Comment on the correct use of continuum solvent models (J. Phys. Chem. A 2010, 114, 13442-13444). One should proceed as follows using gaussian 09: 1. Optimize structure in vacuum and do frequency analysis, from this one can find the free energy correction in the gas phase (dGcorr_gas) 2.Optimize the structure in solvent if you are using another solvent model than SMD I think you should add the keyword cav, dis and rep. The energy you get includes all corrections, also the non electrostatic ones. So this it is actually E_solv + Gnes from the above paper. 3. So to find the free energy in solvent one can simply add everything: dGcorr_gas + E_solv + Gnes. I hope that helps, Servaas On Thu, 2011-04-28 at 19:53 +0200, Arne Dieckmann adieckma[#]googlemail.com wrote: > Sent to CCL by: Arne Dieckmann [adieckma ~ googlemail.com] > Dear Dave, > > I am aware of that. However, as I understand it frequency calculations should be done in vacuum as the equations are derived from an ideal gas assumption. > Am I wrong here? And what would be the energy I need to use from the PCM calculation? > > Cheers, > Arne > > On Apr 28, 2011, at 17:01, "Close, David M. CLOSED^mail.etsu.edu" wrote: > > > > > Sent to CCL by: "Close, David M." [CLOSED++mail.etsu.edu] > > Arne: > > You need to do a frequency calculation and then you will have all the thermodynamic parameters including the free energy, the zero-point energy, etc. > > Regards, Dave Close > > > > -----Original Message----- > >> From: owner-chemistry+closed==etsu.edu(!)ccl.net [mailto:owner-chemistry+closed==etsu.edu(!)ccl.net] On Behalf Of Arne Dieckmann adieckma]_[googlemail.com > > Sent: Thursday, April 28, 2011 8:53 AM > > To: Close, David M. > > Subject: CCL:G: implicit solvation > > > > > > Sent to CCL by: "Arne Dieckmann" [adieckma---googlemail.com] > > Dear all, > > > > I am performing Gaussian calculations using implicit solvation (CPCM). Afterwards, I would like to apply thermal corrections from gas phase calculations to obtain free energy differences of certain molecules. The Gaussian output contains several energy values when using implicit solvation, e.g. "After PCM corrections, the SCF energy is -193.093761350" and "Total free energy in solution with all non electrostatic terms". Which one would I use to add the correction for free energy? > > > > > > Thanks in advance, > > Arnehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Fri Apr 29 05:00:01 2011 From: "Sanjay Bharathwaj computationalchemist{=}gmail.com" To: CCL Subject: CCL: Zipping the folders Message-Id: <-44486-110429043541-25133-554A4mNhGfU5d+v3ygu7tA:_:server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=000e0cd5c66ea044d504a20a8eeb Date: Fri, 29 Apr 2011 10:35:33 +0200 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist a gmail.com] --000e0cd5c66ea044d504a20a8eeb Content-Type: text/plain; charset=ISO-8859-1 Dear Colleagues, I have lots of folder and wish to zip it. I know one can do, by entering each folder and giving the comment tar -cf ./foldername or gzip ./folder name and the output here is single gip file with enormous size. I don't want this single file. Instead, i wish to zip all the files in the folder and that allows me to access each of the zip files whenever i need it. (i.e) Assuming the Mainfolder has two subfolders which has 10 and 15 files respectively as follows Mainfolder /folder1/10 files /folder2/15 files gzip/tar gives me mainfolder.zip as one file. But i am looking for some command which does the following Mainfolder /folder1/10 files.zip /folder2/15 files.zip So all the folders remain uncompressed while just the files get zipped. The one way is to go through each folder and use gzip. But that's painful job as i have more than 100's of folder. Does any one know which command should i use for this. Best regards, Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --000e0cd5c66ea044d504a20a8eeb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear=A0Colleagues,

I have lots of folder and wish to zip= it.

I know one can do, by entering each folder an= d giving the comment
tar -cf ./foldername=A0or =A0gzip ./folder n= ame
and the output here is single gip file with enormous size.
<= br>
I don't want this single file.

I= nstead, i wish to zip all the files in the folder and=A0
that all= ows me to access each of the zip files whenever i need it.


(i.e)=A0Assuming the Mainfolder has two = subfolders=A0
which has 10 and 15 files respectively as follows

Mainfolder =A0 /folder1/10 files
=A0=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0/folder2/15 files

gzip/tar gives me mainfolder.zip as one file.

But i am looking for some command which=A0
does t= he following

Mainfolder =A0 /folder1/10 files.zip
=A0=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0/folder2/15 files.zip

So all the = folders remain uncompressed while just the
files get zipped.

The one way is to go through each folder and use
gzip. But that&#= 39;s painful job as i have more than 100's of folder.=A0
Does= any one know which command should i use for this.

Best regards,
Sanjay



=

--
Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendr= a Institute of Technology,
India.
--000e0cd5c66ea044d504a20a8eeb-- From owner-chemistry@ccl.net Fri Apr 29 06:01:00 2011 From: "mirage . m.o.m]_[live.fr" To: CCL Subject: CCL:G: FW CCL:G: install gaussian09 on ubuntu 9.04 Message-Id: <-44487-110429055732-9335-qohBWnZLWN1gX2CvNlL6Yw .. server.ccl.net> X-Original-From: "mirage ." Content-Type: multipart/alternative; boundary="_e59ad892-b68e-45eb-964a-428cc8e8a01d_" Date: Fri, 29 Apr 2011 09:57:23 +0000 MIME-Version: 1.0 Sent to CCL by: "mirage ." [m.o.m{=}live.fr] --_e59ad892-b68e-45eb-964a-428cc8e8a01d_ Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit HI, Thanks for reply my archtecture is i686 , in bldg09 there is no i686 but i386!! > From: owner-chemistry[#]ccl.net > To: m.o.m[#]live.fr > Subject: CCL:G: FW CCL:G: install gaussian09 on ubuntu 9.04 > Date: Fri, 29 Apr 2011 09:21:02 +0800 > > > Sent to CCL by: Fuming Ying [fmying[*]gmail.com] > There are lines in bsd/bldg09 like: > > ... > cc -o gau-machine $machflag bsd/machine.c > ... > set x = `gau-machine` > echo "machine type is $x" > ... > else if ("$x" == "amd64") then > ... > > This part is written to check the architecture of your machine to make > your Gaussian work properly. > Looks like either variable x is not saved or gau-machine cannot be > compiled correctly. Check the errors in your "make.log" to see if there > is some error occured when compiling gau-machine. What's more, could you > also check if compilers are prepared? like icc/ifort, gcc/gfortran etc.? > And the architecture of your machine with command > uname -a > > BTW, is it essential to recompile Gaussian 09? Is your Gaussian 09 > binary package? If so, there will NOT be any source code file in it and > compilation will definitely go wrong. > > > Best regards, > Fuming Ying > > $BP2(B 2011/4/29 2:48, Serge Lavilier m.o.m*_*live.fr $B > Sent to CCL by: "Serge Lavilier" [m.o.m .. live.fr] > > Hi > > Thanks for reply > > For $ sudo apt-get install tcsh > > Ubuntu tel me that i have the last version !! > > > > After, i doing > > > > > > $cd $g09root > > $chgrp -R Serge g09 > > $cd g09 > > $./bsd/install > > $source $g09root/g09/bsd/g09.profile there is no error message > > $bsd/bldg09 >&make.log > > > > $ tail make.log > > > > if ( == hi_osf ) then > > if ( == hal ) then > > if ( == alpha-linux ) then > > if ( == ia64 ) then > > if ( == mac ) then > > if ( == gp7kf ) then > > exit bldg09 is confused > > exit: Expression Syntax. > > > > What's wrong ? > > > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl##st-andrews.ac.uk] > > If he removes the "exit" in the third line, it should work. > > He's starting csh and then exits it again, before trying to > > source some csh commands. > > H. > > On 04/28/2011 02:48 PM, Fuming Ying fmying{}gmail.com wrote: > > > > > > Sent to CCL by: Fuming Ying [fmying!A!gmail.com] > > > 2011/4/28 14:43, Serge Lavilier m-22#%#hotmail.fr > > : > > >> Sent to CCL by: "Serge Lavilier" [m-22]~[hotmail.fr] > > >> Hi, > > >> I want to install gaussian09 on ubuntu 9.04 > > >> > > >> $/bin/csh > > >> %setenv g09root "/home/Serge/Gaussian" > > >> %exit > > >> $cd $g09root > > >> $chgrp -R Serge g09 > > >> $cd g09 > > >> $./bsd/install > > >> $source $g09root/g09/bsd/g09.login > > >> > > >> line 25: Erreur de syntaxe prs du symbole inattendu setenv > > >> bash: /home/Serge/gaussian/g09/bsd/g09.login: line 25: `if (! $?PGI ) > > setenv PGI /usr/pgi' > > > It should be the problem that the keyword "setenv" can be > > executed properly. > > > Have you checked that the proper C shell (the package name should be > > > tcsh) is installed in your ubuntu system? C shell will NOT be installed > > > in Ubuntu by default so that you should install it manually with command > > > > > > sudo apt-get install tcsh > > > > > > Alternatively, there is a scripit "$g09root/g09/bsd/g03.profile" > > which > > > is written in Bash. Since bash is installed by default in Ubuntu, you > > > can work with Gaussian 09 under Bash instead of C shell. > > > > > > After installation, type this command > > > . $g09root/g09/bsd/g09.profile > > > to set the environment variables under Bash before using g09. Of course, > > > $g09root should be meaningful. This command can also be written in > > > $HOME/.bashrc so that you don't have to type it every time you log in. > > > > > > Best regards, > > > Fuming Ying > > > > > >> What's Wrong?> > > > > > -- > > Herbert Fruchtl > > Senior Scientific Computing Officer > > School of Chemistry, School of Mathematics and Statistics > > University of St Andrews > > -- > > The University of St Andrews is a charity registered in Scotland: > > No SC013532> > --_e59ad892-b68e-45eb-964a-428cc8e8a01d_ Content-Type: text/html; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit HI,
Thanks for reply
 my archtecture is i686 , in bldg09 there is no i686 but i386!!

> From: owner-chemistry[#]ccl.net
> To: m.o.m[#]live.fr
> Subject: CCL:G: FW CCL:G: install gaussian09 on ubuntu 9.04
> Date: Fri, 29 Apr 2011 09:21:02 +0800
>
>
> Sent to CCL by: Fuming Ying [fmying[*]gmail.com]
> There are lines in bsd/bldg09 like:
>
> ...
> cc -o gau-machine $machflag bsd/machine.c
> ...
> set x = `gau-machine`
> echo "machine type is $x"
> ...
> else if ("$x" == "amd64") then
> ...
>
> This part is written to check the architecture of your machine to make
> your Gaussian work properly.
> Looks like either variable x is not saved or gau-machine cannot be
> compiled correctly. Check the errors in your "make.log" to see if there
> is some error occured when compiling gau-machine. What's more, could you
> also check if compilers are prepared? like icc/ifort, gcc/gfortran etc.?
> And the architecture of your machine with command
> uname -a
>
> BTW, is it essential to recompile Gaussian 09? Is your Gaussian 09
> binary package? If so, there will NOT be any source code file in it and
> compilation will definitely go wrong.
>
>
> Best regards,
> Fuming Ying
>
> $BP2(B 2011/4/29 2:48, Serge Lavilier m.o.m*_*live.fr $B> > Sent to CCL by: "Serge Lavilier" [m.o.m .. live.fr]
> > Hi
> > Thanks for reply
> > For $ sudo apt-get install tcsh
> > Ubuntu tel me that i have the last version !!
> >
> > After, i doing
> >
> >
> > $cd $g09root
> > $chgrp -R Serge g09
> > $cd g09
> > $./bsd/install
> > $source $g09root/g09/bsd/g09.profile there is no error message
> > $bsd/bldg09 >&make.log
> >
> > $ tail make.log
> >
> > if ( == hi_osf ) then
> > if ( == hal ) then
> > if ( == alpha-linux ) then
> > if ( == ia64 ) then
> > if ( == mac ) then
> > if ( == gp7kf ) then
> > exit bldg09 is confused
> > exit: Expression Syntax.
> >
> > What's wrong ?
> >
> > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl##st-andrews.ac.uk]
> > If he removes the "exit" in the third line, it should work.
> > He's starting csh and then exits it again, before trying to
> > source some csh commands.
> > H.
> > On 04/28/2011 02:48 PM, Fuming Ying fmying{}gmail.com wrote:
> > >
> > > Sent to CCL by: Fuming Ying [fmying!A!gmail.com]
> > > 2011/4/28 14:43, Serge Lavilier m-22#%#hotmail.fr
> > :
> > >> Sent to CCL by: "Serge Lavilier" [m-22]~[hotmail.fr]
> > >> Hi,
> > >> I want to install gaussian09 on ubuntu 9.04
> > >>
> > >> $/bin/csh
> > >> %setenv g09root "/home/Serge/Gaussian"
> > >> %exit
> > >> $cd $g09root
> > >> $chgrp -R Serge g09
> > >> $cd g09
> > >> $./bsd/install
> > >> $source $g09root/g09/bsd/g09.login
> > >>
> > >> line 25: Erreur de syntaxe prs du symbole inattendu setenv
> > >> bash: /home/Serge/gaussian/g09/bsd/g09.login: line 25: `if (! $?PGI )
> > setenv PGI /usr/pgi'
> > > It should be the problem that the keyword "setenv" can be
> > executed properly.
> > > Have you checked that the proper C shell (the package name should be
> > > tcsh) is installed in your ubuntu system? C shell will NOT be installed
> > > in Ubuntu by default so that you should install it manually with command
> > >
> > > sudo apt-get install tcsh
> > >
> > > Alternatively, there is a scripit "$g09root/g09/bsd/g03.profile"
> > which
> > > is written in Bash. Since bash is installed by default in Ubuntu, you
> > > can work with Gaussian 09 under Bash instead of C shell.
> > >
> > > After installation, type this command
> > > . $g09root/g09/bsd/g09.profile
> > > to set the environment variables under Bash before using g09. Of course,
> > > $g09root should be meaningful. This command can also be written in
> > > $HOME/.bashrc so that you don't have to type it every time you log in.
> > >
> > > Best regards,
> > > Fuming Ying
> > >
> > >> What's Wrong?>
> > >
> > --
> > Herbert Fruchtl
> > Senior Scientific Computing Officer
> > School of Chemistry, School of Mathematics and Statistics
> > University of St Andrews
> > --
> > The University of St Andrews is a charity registered in Scotland:
> > No SC013532>
> >
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
--_e59ad892-b68e-45eb-964a-428cc8e8a01d_-- From owner-chemistry@ccl.net Fri Apr 29 06:36:00 2011 From: "Arne Dieckmann adieckma .. googlemail.com" To: CCL Subject: CCL:G: implicit solvation Message-Id: <-44488-110429060303-13938-/XpCIFhiSbd64I78zd8lHw\a/server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 29 Apr 2011 12:02:51 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Arne Dieckmann [adieckma|*|googlemail.com] Dear Servaas, thanks for your reply, that' the procedure I applied. However, looking at some examples I found some telling to use the energy given by ""After PCM corrections, the SCF energy is" and some the energy given by "Total free energy in solution with all non electrostatic terms" (Gaussian03). I was wondering if the last one is actually the one to use because the energy of transition states I am investigating is actually raised rather than lowered in solution (reaction type is a nucleophilic attack). What's your point on this? Thanks, Arne On Apr 29, 2011, at 10:08 AM, servaas servaas.michielssens**student.kuleuven.be wrote: > > Sent to CCL by: servaas [servaas.michielssens[*]student.kuleuven.be] > According to the procedure described in Comment on the correct use of > continuum solvent models (J. Phys. Chem. A 2010, 114, 13442-13444). One > should proceed as follows using gaussian 09: > 1. Optimize structure in vacuum and do frequency analysis, from this one > can find the free energy correction in the gas phase (dGcorr_gas) > 2.Optimize the structure in solvent if you are using another solvent > model than SMD I think you should add the keyword cav, dis and rep. The > energy you get includes all corrections, also the non electrostatic > ones. So this it is actually E_solv + Gnes from the above paper. > 3. So to find the free energy in solvent one can simply add everything: > dGcorr_gas + E_solv + Gnes. > > > I hope that helps, > > Servaas > > On Thu, 2011-04-28 at 19:53 +0200, Arne Dieckmann > adieckma[#]googlemail.com wrote: >> Sent to CCL by: Arne Dieckmann [adieckma ~ googlemail.com] >> Dear Dave, >> >> I am aware of that. However, as I understand it frequency calculations should be done in vacuum as the equations are derived from an ideal gas assumption. > >> Am I wrong here? And what would be the energy I need to use from the PCM calculation? >> >> Cheers, >> Arne >> >> On Apr 28, 2011, at 17:01, "Close, David M. CLOSED^mail.etsu.edu" wrote: >> >>> >>> Sent to CCL by: "Close, David M." [CLOSED++mail.etsu.edu] >>> Arne: >>> You need to do a frequency calculation and then you will have all the thermodynamic parameters including the free energy, the zero-point energy, etc. >>> Regards, Dave Close >>> >>> -----Original Message----- >>>> From: owner-chemistry+closed==etsu.edu(!)ccl.net [mailto:owner-chemistry+closed==etsu.edu(!)ccl.net] On Behalf Of Arne Dieckmann adieckma]_[googlemail.com >>> Sent: Thursday, April 28, 2011 8:53 AM >>> To: Close, David M. >>> Subject: CCL:G: implicit solvation >>> >>> >>> Sent to CCL by: "Arne Dieckmann" [adieckma---googlemail.com] >>> Dear all, >>> >>> I am performing Gaussian calculations using implicit solvation (CPCM). Afterwards, I would like to apply thermal corrections from gas phase calculations to obtain free energy differences of certain molecules. The Gaussian output contains several energy values when using implicit solvation, e.g. "After PCM corrections, the SCF energy is -193.093761350" and "Total free energy in solution with all non electrostatic terms". Which one would I use to add the correction for free energy? >>> >>> >>> Thanks in advance, >>> Arnehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Fri Apr 29 07:10:00 2011 From: "steinbrt.=.rci.rutgers.edu" To: CCL Subject: CCL: Zipping the folders Message-Id: <-44489-110429062752-8494-7/BvtmUMduWwQW4IAfxbQg=server.ccl.net> X-Original-From: steinbrt(a)rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 29 Apr 2011 06:27:43 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: steinbrt]|[rci.rutgers.edu I doubt that this question is CCL material, but 'man gzip' shows: -r --recursive Travel the directory structure recursively. If any of the file names specified on the command line are directories, gzip will descend into the directory and compress all the files it finds there (or decompress them in the case of gunzip ). Thomas On Fri, April 29, 2011 4:35 am, Sanjay Bharathwaj computationalchemist{=}gmail.com wrote: > Dear Colleagues, > > I have lots of folder and wish to zip it. > > I know one can do, by entering each folder and giving the comment > tar -cf ./foldername or gzip ./folder name > and the output here is single gip file with enormous size. > > I don't want this single file. > > Instead, i wish to zip all the files in the folder and > that allows me to access each of the zip files whenever i need it. > > > (i.e) Assuming the Mainfolder has two subfolders > which has 10 and 15 files respectively as follows > > Mainfolder /folder1/10 files > /folder2/15 files > > gzip/tar gives me mainfolder.zip as one file. > > But i am looking for some command which > does the following > > Mainfolder /folder1/10 files.zip > /folder2/15 files.zip > > So all the folders remain uncompressed while just the > files get zipped. > > The one way is to go through each folder and use > gzip. But that's painful job as i have more than 100's of folder. > Does any one know which command should i use for this. > > Best regards, > Sanjay > > > > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. > Dr. Thomas Steinbrecher formerly at the BioMaps Institute Rutgers University 610 Taylor Rd. Piscataway, NJ 08854 From owner-chemistry@ccl.net Fri Apr 29 08:27:00 2011 From: "servaas servaas.michielssens%a%student.kuleuven.be" To: CCL Subject: CCL:G: implicit solvation Message-Id: <-44490-110429082552-19992-/MWbWL/AsRsw0laBZtNizA-*-server.ccl.net> X-Original-From: servaas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Fri, 29 Apr 2011 14:25:38 +0200 Mime-Version: 1.0 Sent to CCL by: servaas [servaas.michielssens|-|student.kuleuven.be] I am not so familiar with the Gaussian 03 output which is different for PCM than gaussian 09. When I look in the g03 manual I think one should use: Total free energy in solution with all non electrostatic terms. This is equal to E_solv + Gnes. The energy output is only with electrostatic terms in contrast to Gaussian 09 where all terms are included in the final energy. Do you mean the energy is higher compared to the reactants or higher than the TS in vacuum? Whether this is logical depends on the details of the molecules you are studying. kind regards, Servaas On Fri, 2011-04-29 at 12:02 +0200, Arne Dieckmann adieckma .. googlemail.com wrote: > Sent to CCL by: Arne Dieckmann [adieckma|*|googlemail.com] > Dear Servaas, > > thanks for your reply, that' the procedure I applied. However, looking at some examples I found some telling to use the energy given by ""After PCM corrections, the SCF energy is" and some the energy given by "Total free energy in solution with all non electrostatic terms" (Gaussian03). I was wondering if the last one is actually the one to use because the energy of transition states I am investigating is actually raised rather than lowered in solution (reaction type is a nucleophilic attack). What's your point on this? > > > Thanks, > Arne > > > On Apr 29, 2011, at 10:08 AM, servaas servaas.michielssens**student.kuleuven.be wrote: > > > > > Sent to CCL by: servaas [servaas.michielssens[*]student.kuleuven.be] > > According to the procedure described in Comment on the correct use of > > continuum solvent models (J. Phys. Chem. A 2010, 114, 13442-13444). One > > should proceed as follows using gaussian 09: > > 1. Optimize structure in vacuum and do frequency analysis, from this one > > can find the free energy correction in the gas phase (dGcorr_gas) > > 2.Optimize the structure in solvent if you are using another solvent > > model than SMD I think you should add the keyword cav, dis and rep. The > > energy you get includes all corrections, also the non electrostatic > > ones. So this it is actually E_solv + Gnes from the above paper. > > 3. So to find the free energy in solvent one can simply add everything: > > dGcorr_gas + E_solv + Gnes. > > > > > > I hope that helps, > > > > Servaas > > > > On Thu, 2011-04-28 at 19:53 +0200, Arne Dieckmann > > adieckma[#]googlemail.com wrote: > >> Sent to CCL by: Arne Dieckmann [adieckma ~ googlemail.com] > >> Dear Dave, > >> > >> I am aware of that. However, as I understand it frequency calculations should be done in vacuum as the equations are derived from an ideal gas assumption. > > > >> Am I wrong here? And what would be the energy I need to use from the PCM calculation? > >> > >> Cheers, > >> Arne > >> > >> On Apr 28, 2011, at 17:01, "Close, David M. CLOSED^mail.etsu.edu" wrote: > >> > >>> > >>> Sent to CCL by: "Close, David M." [CLOSED++mail.etsu.edu] > >>> Arne: > >>> You need to do a frequency calculation and then you will have all the thermodynamic parameters including the free energy, the zero-point energy, etc. > >>> Regards, Dave Close > >>> > >>> -----Original Message----- > >>>> From: owner-chemistry+closed==etsu.edu(!)ccl.net [mailto:owner-chemistry+closed==etsu.edu(!)ccl.net] On Behalf Of Arne Dieckmann adieckma]_[googlemail.com > >>> Sent: Thursday, April 28, 2011 8:53 AM > >>> To: Close, David M. > >>> Subject: CCL:G: implicit solvation > >>> > >>> > >>> Sent to CCL by: "Arne Dieckmann" [adieckma---googlemail.com] > >>> Dear all, > >>> > >>> I am performing Gaussian calculations using implicit solvation (CPCM). Afterwards, I would like to apply thermal corrections from gas phase calculations to obtain free energy differences of certain molecules. The Gaussian output contains several energy values when using implicit solvation, e.g. "After PCM corrections, the SCF energy is -193.093761350" and "Total free energy in solution with all non electrostatic terms". Which one would I use to add the correction for free energy? > >>> > >>> > >>> Thanks in advance, > >>> Arnehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Fri Apr 29 09:16:00 2011 From: "Arne Dieckmann adieckma]=[googlemail.com" To: CCL Subject: CCL:G: implicit solvation Message-Id: <-44491-110429091504-403-eGV+40BO/Usxv32d4ASUvw_._server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 29 Apr 2011 15:14:52 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Arne Dieckmann [adieckma[*]googlemail.com] Alright, that is what I thought as well. The energy of transition states of some nucleophilic attacks relative to the energy of the precursors is higher in solution. This is surprising as I anticipated a polar solvent like acetonitrile to lower the energy of these interactions. I would expect stabilizing interactions with any polar solvent for nucleophilic attacks of polar molecules in general. On Apr 29, 2011, at 2:25 PM, servaas servaas.michielssens%a%student.kuleuven.be wrote: > > Sent to CCL by: servaas [servaas.michielssens|-|student.kuleuven.be] > I am not so familiar with the Gaussian 03 output which is different > for PCM than gaussian 09. When I look in the g03 manual I think one should > use: Total free energy in solution with all non electrostatic terms. > This is equal to E_solv + Gnes. The energy output is only with electrostatic > terms in contrast to Gaussian 09 where all terms are included in the final energy. > > > Do you mean the energy is higher compared to the reactants or higher > than the TS in vacuum? Whether this is logical depends on the details of > the molecules you are studying. > > kind regards, > > Servaas > > On Fri, 2011-04-29 at 12:02 +0200, Arne Dieckmann adieckma .. > googlemail.com wrote: >> Sent to CCL by: Arne Dieckmann [adieckma|*|googlemail.com] >> Dear Servaas, >> >> thanks for your reply, that' the procedure I applied. However, looking at some examples I found some telling to use the energy given by ""After PCM corrections, the SCF energy is" and some the energy given by "Total free energy in solution with all non electrostatic terms" (Gaussian03). I was wondering if the last one is actually the one to use because the energy of transition states I am investigating is actually raised rather than lowered in solution (reaction type is a nucleophilic attack). What's your point on this? >> >> >> Thanks, >> Arne >> >> >> On Apr 29, 2011, at 10:08 AM, servaas servaas.michielssens**student.kuleuven.be wrote: >> >>> >>> Sent to CCL by: servaas [servaas.michielssens[*]student.kuleuven.be] >>> According to the procedure described in Comment on the correct use of >>> continuum solvent models (J. Phys. Chem. A 2010, 114, 13442-13444). One >>> should proceed as follows using gaussian 09: >>> 1. Optimize structure in vacuum and do frequency analysis, from this one >>> can find the free energy correction in the gas phase (dGcorr_gas) >>> 2.Optimize the structure in solvent if you are using another solvent >>> model than SMD I think you should add the keyword cav, dis and rep. The >>> energy you get includes all corrections, also the non electrostatic >>> ones. So this it is actually E_solv + Gnes from the above paper. >>> 3. So to find the free energy in solvent one can simply add everything: >>> dGcorr_gas + E_solv + Gnes. >>> >>> >>> I hope that helps, >>> >>> Servaas >>> >>> On Thu, 2011-04-28 at 19:53 +0200, Arne Dieckmann >>> adieckma[#]googlemail.com wrote: >>>> Sent to CCL by: Arne Dieckmann [adieckma ~ googlemail.com] >>>> Dear Dave, >>>> >>>> I am aware of that. However, as I understand it frequency calculations should be done in vacuum as the equations are derived from an ideal gas assumption. >>> >>>> Am I wrong here? And what would be the energy I need to use from the PCM calculation? >>>> >>>> Cheers, >>>> Arne >>>> >>>> On Apr 28, 2011, at 17:01, "Close, David M. CLOSED^mail.etsu.edu" wrote: >>>> >>>>> >>>>> Sent to CCL by: "Close, David M." [CLOSED++mail.etsu.edu] >>>>> Arne: >>>>> You need to do a frequency calculation and then you will have all the thermodynamic parameters including the free energy, the zero-point energy, etc. >>>>> Regards, Dave Close >>>>> >>>>> -----Original Message----- >>>>>> From: owner-chemistry+closed==etsu.edu(!)ccl.net [mailto:owner-chemistry+closed==etsu.edu(!)ccl.net] On Behalf Of Arne Dieckmann adieckma]_[googlemail.com >>>>> Sent: Thursday, April 28, 2011 8:53 AM >>>>> To: Close, David M. >>>>> Subject: CCL:G: implicit solvation >>>>> >>>>> >>>>> Sent to CCL by: "Arne Dieckmann" [adieckma---googlemail.com] >>>>> Dear all, >>>>> >>>>> I am performing Gaussian calculations using implicit solvation (CPCM). Afterwards, I would like to apply thermal corrections from gas phase calculations to obtain free energy differences of certain molecules. The Gaussian output contains several energy values when using implicit solvation, e.g. "After PCM corrections, the SCF energy is -193.093761350" and "Total free energy in solution with all non electrostatic terms". Which one would I use to add the correction for free energy? >>>>> >>>>> >>>>> Thanks in advance, >>>>> Arnehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Fri Apr 29 09:51:01 2011 From: "Igor Filippov Contr igorf#%#helix.nih.gov" To: CCL Subject: CCL: Zipping the folders Message-Id: <-44492-110429093531-9382-7g0sJY/SmDgupaJ2xVOi2Q,,server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Fri, 29 Apr 2011 09:31:08 -0400 MIME-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf+*+helix.nih.gov] Why don't you just do something like find . -type f -not -name "*.gz" -exec gzip {} \; (you need to check man find for precise syntax of course)? Regards, Igor On Fri, 2011-04-29 at 04:35 -0400, Sanjay Bharathwaj computationalchemist{=}gmail.com wrote: > Dear Colleagues, > > > I have lots of folder and wish to zip it. > > > I know one can do, by entering each folder and giving the comment > tar -cf ./foldername or gzip ./folder name > and the output here is single gip file with enormous size. > > > I don't want this single file. > > > Instead, i wish to zip all the files in the folder and > that allows me to access each of the zip files whenever i need it. > > > > > (i.e) Assuming the Mainfolder has two subfolders > which has 10 and 15 files respectively as follows > > > Mainfolder /folder1/10 files > /folder2/15 files > > > gzip/tar gives me mainfolder.zip as one file. > > > But i am looking for some command which > does the following > > > Mainfolder /folder1/10 files.zip > /folder2/15 files.zip > > > So all the folders remain uncompressed while just the > files get zipped. > > > The one way is to go through each folder and use > gzip. But that's painful job as i have more than 100's of folder. > Does any one know which command should i use for this. > > > Best regards, > Sanjay > > > > > > > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. > From owner-chemistry@ccl.net Fri Apr 29 10:26:00 2011 From: "Fuming Ying fmying!=!gmail.com" To: CCL Subject: CCL:G: FW CCL:G: install gaussian09 on ubuntu 9.04 Message-Id: <-44493-110429080108-5459-1+HrRAfPm8GP427ipzO9ow||server.ccl.net> X-Original-From: Fuming Ying Content-Type: multipart/alternative; boundary="------------080806030605000505040501" Date: Fri, 29 Apr 2011 20:00:45 +0800 MIME-Version: 1.0 Sent to CCL by: Fuming Ying [fmying ~~ gmail.com] This is a multi-part message in MIME format. --------------080806030605000505040501 Content-Type: text/plain; charset=ISO-2022-JP Content-Transfer-Encoding: 7bit The lines I listed before tell us that the information of the architecture is stored in variable "$x". As you shew us: if ( == hi_osf ) then we know that "$x" cannot provide any information of your architecture. This could be the reason that the content of $x is blank, which means either "gau-machine" cannot detect the correct architecture, or the compilation of gau-machine cannot be done correctly. You told us that $source $g09root/g09/bsd/g09.profile there is no error message so check if you can run g09 after this command if you are in bash. To run g09, you also need to set the variable $GAUSS_SCRDIR by command $export GAUSS_SCRDIR=yourdir/ (in bash) or $setenv GAUSS_SCRDIR yourdir/ (in tcsh) where yourdir is the directory defined by yourself. Make sure that "yourdir" exists!!! Generally speaking, your g09 shoul.d be able to work after this command and setting variable $GAUSS_SCRDIR if your g09 is binary. Compilation is available ONLY for source code package! $BP2(B 2011/4/29 17:57, mirage . m.o.m]_[live.fr $B HI, > Thanks for reply > my archtecture is i686 , in bldg09 there is no i686 but i386!! > > > From: owner-chemistry_._ccl.net > > To: m.o.m_._live.fr > > Subject: CCL:G: FW CCL:G: install gaussian09 on ubuntu 9.04 > > Date: Fri, 29 Apr 2011 09:21:02 +0800 > > > > > > Sent to CCL by: Fuming Ying [fmying[*]gmail.com] > > There are lines in bsd/bldg09 like: > > > > ... > > cc -o gau-machine $machflag bsd/machine.c > > ... > > set x = `gau-machine` > > echo "machine type is $x" > > ... > > else if ("$x" == "amd64") then > > ... > > > > This part is written to check the architecture of your machine to make > > your Gaussian work properly. > > Looks like either variable x is not saved or gau-machine cannot be > > compiled correctly. Check the errors in your "make.log" to see if there > > is some error occured when compiling gau-machine. What's more, could you > > also chec! k if compilers are prepared? like icc/ifort, gcc/gfortran > etc.? > > And the architecture of your machine with command > > uname -a > > > > BTW, is it essential to recompile Gaussian 09? Is your Gaussian 09 > > binary package? If so, there will NOT be any source code file in it and > > compilation will definitely go wrong. > > > > > > Best regards, > > Fuming Ying > > > > $BP2(B 2011/4/29 2:48, Serge Lavilier m.o.m*_*live.fr $B > > Sent to CCL by: "Serge Lavilier" [m.o.m .. live.fr] > > > Hi > > > Thanks for reply > > > For $ sudo apt-get install tcsh > > > Ubuntu tel me that i have the last version !! > > > > > > After, i doing > > > > > > > > > $cd $g09root > > > $chgrp -R Serge g09 > > > $cd g09 > > > $./bsd/install > > > $source $g09root/g09/bsd/g09.profile there is no error message > > > $bsd/bldg0! 9 >&make.log > > > > > > $ tail make.log> > > > > if ( == hi_osf ) then > > > if ( == hal ) then > > > if ( == alpha-linux ) then > > > if ( == ia64 ) then > > > if ( == mac ) then > > > if ( == gp7kf ) then > > > exit bldg09 is confused > > > exit: Expression Syntax. > > > > > > What's wrong ? > > > > > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl##st-andrews.ac.uk] > > > If he removes the "exit" in the third line, it should work. > > > He's starting csh and then exits it again, before trying to > > > source some csh commands. > > > H. > > > On 04/28/2011 02:48 PM, Fuming Ying fmying{}gmail.com wrote: > > > > > > > > Sent to CCL by: Fuming Ying [fmying!A!gmail.com] > > > > 2011/4/28 14:43, Serge Lavilier m-22#%#hotmail.fr > > > : > > > >> Sent to CCL by: "Serge Lavilier" [m-22]~[hotmail.fr] > > > >> Hi,> > >> I want to install gaussian09 on ubuntu 9.04 > > > >> > > > >> $/bin/csh > > > >> %setenv g09root "/home/Serge/Gaussian" > > > >> %exit > > > >> $cd $g09root > > > >> $chgrp -R Serge g09 > > > >> $cd g09 > > > >> $./bsd/install > > > >> $source $g09root/g09/bsd/g09.login > > > >> > > > >> line 25: Erreur de syntaxe prs du symbole inattendu setenv > > > >> bash: /home/Serge/gaussian/g09/bsd/g09.login: line 25: `if (! > $?PGI ) > > > setenv PGI /usr/pgi' > > > > It should be the problem that the keyword "setenv" can be > > > executed properly. > > > > Have you checked that the proper C shell (the package name should be > > > > tcsh) is installed in your ubuntu system? C shell will NOT be > installed > > > > in Ubuntu by default so th! at you should install it manually > with command > > > > > &g! t; > > sudo apt-get install tcsh > > > > > > > > Alternatively, there is a scripit "$g09root/g09/bsd/g03.profile" > > > which > > > > is written in Bash. Since bash is installed by default in > Ubuntu, you > > > > can work with Gaussian 09 under Bash instead of C shell. > > > > > > > > After installation, type this command > > > > . $g09root/g09/bsd/g09.profile > > > > to set the environment variables under Bash before using g09. Of > course, > > > > $g09root should be meaningful. This command can also be written in > > > > $HOME/.bashrc so that you don't have to type it every time you > log in. > > > > > > > > Best regards, > > > > Fuming Ying > > > > > > > >> What's Wrong?> > > > > > > > -- > > > Herbert Fruchtl > > > Senior Scientific Computing Officer > >! > School of Chemistry, School of Mathematics and Statistics > > > University of St Andrews > > > -- > > > The University of St Andrews is a charity registered in Scotland: > > > No SC013532> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > --------------080806030605000505040501 Content-Type: text/html; charset=ISO-2022-JP Content-Transfer-Encoding: 7bit The lines I listed before tell us that the information of the architecture is stored in variable "$x".
As you shew us:

if ( == hi_osf ) then

we know that "$x" cannot provide any information of your architecture. This could be the reason that the content of $x is blank, which means either "gau-machine" cannot detect the correct architecture, or the compilation of gau-machine cannot be done correctly.

You told us that

$source $g09root/g09/bsd/g09.profile there is no error message

so check if you can run g09 after this command if you are in bash.

To run g09, you also need to set the variable $GAUSS_SCRDIR by command

$export GAUSS_SCRDIR=yourdir/ (in bash)

or

$setenv GAUSS_SCRDIR yourdir/ (in tcsh)

where yourdir is the directory defined by yourself. Make sure that "yourdir" exists!!!

Generally speaking, your g09 shoul.d be able to work after this command and setting variable $GAUSS_SCRDIR if your g09 is binary. Compilation is available ONLY for source code package!


$BP2(B 2011/4/29 17:57, mirage . m.o.m]_[live.fr $B HI,
Thanks for reply
 my archtecture is i686 , in bldg09 there is no i686 but i386!!

> From: owner-chemistry_._ccl.net
> To: m.o.m_._live.fr
> Subject: CCL:G: FW CCL:G: install gaussian09 on ubuntu 9.04
> Date: Fri, 29 Apr 2011 09:21:02 +0800
>
>
> Sent to CCL by: Fuming Ying [fmying[*]gmail.com]
> There are lines in bsd/bldg09 like:
>
> ...
> cc -o gau-machine $machflag bsd/machine.c
> ...
> set x = `gau-machine`
> echo "machine type is $x"
> ...
> else if ("$x" == "amd64") then
> ...
>
> This part is written to check the architecture of your machine to make
> your Gaussian work properly.
> Looks like either variable x is not saved or gau-machine cannot be
> compiled correctly. Check the errors in your "make.log" to see if there
> is some error occured when compiling gau-machine. What's more, could you
> also chec! k if compilers are prepared? like icc/ifort, gcc/gfortran etc.?
> And the architecture of your machine with command
> uname -a
>
> BTW, is it essential to recompile Gaussian 09? Is your Gaussian 09
> binary package? If so, there will NOT be any source code file in it and
> compilation will definitely go wrong.
>
>
> Best regards,
> Fuming Ying
>
> $BP2(B 2011/4/29 2:48, Serge Lavilier m.o.m*_*live.fr $B > > Sent to CCL by: "Serge Lavilier" [m.o.m .. live.fr]
> > Hi
> > Thanks for reply
> > For $ sudo apt-get install tcsh
> > Ubuntu tel me that i have the last version !!
> >
> > After, i doing
> >
> >
> > $cd $g09root
> > $chgrp -R Serge g09
> > $cd g09
> > $./bsd/install
> > $source $g09root/g09/bsd/g09.profile there is no error message
> > $bsd/bldg0! 9 >&make.log
> >
> > $ tail make.log> >
> > if ( == hi_osf ) then
> > if ( == hal ) then
> > if ( == alpha-linux ) then
> > if ( == ia64 ) then
> > if ( == mac ) then
> > if ( == gp7kf ) then
> > exit bldg09 is confused
> > exit: Expression Syntax.
> >
> > What's wrong ?
> >
> > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl##st-andrews.ac.uk]
> > If he removes the "exit" in the third line, it should work.
> > He's starting csh and then exits it again, before trying to
> > source some csh commands.
> > H.
> > On 04/28/2011 02:48 PM, Fuming Ying fmying{}gmail.com wrote:
> > >
> > > Sent to CCL by: Fuming Ying [fmying!A!gmail.com]
> > > 2011/4/28 14:43, Serge Lavilier m-22#%#hotmail.fr
> > :
> > >> Sent to CCL by: "Serge Lavilier" [m-22]~[hotmail.fr]
> > >> Hi,> > >> I want to install gaussian09 on ubuntu 9.04
> > >>
> > >> $/bin/csh
> > >> %setenv g09root "/home/Serge/Gaussian"
> > >> %exit
> > >> $cd $g09root
> > >> $chgrp -R Serge g09
> > >> $cd g09
> > >> $./bsd/install
> > >> $source $g09root/g09/bsd/g09.login
> > >>
> > >> line 25: Erreur de syntaxe prs du symbole inattendu setenv
> > >> bash: /home/Serge/gaussian/g09/bsd/g09.login: line 25: `if (! $?PGI )
> > setenv PGI /usr/pgi'
> > > It should be the problem that the keyword "setenv" can be
> > executed properly.
> > > Have you checked that the proper C shell (the package name should be
> > > tcsh) is installed in your ubuntu system? C shell will NOT be installed
> > > in Ubuntu by default so th! at you should install it manually with command
> > >
&g! t; > > sudo apt-get install tcsh
> > >
> > > Alternatively, there is a scripit "$g09root/g09/bsd/g03.profile"
> > which
> > > is written in Bash. Since bash is installed by default in Ubuntu, you
> > > can work with Gaussian 09 under Bash instead of C shell.
> > >
> > > After installation, type this command
> > > . $g09root/g09/bsd/g09.profile
> > > to set the environment variables under Bash before using g09. Of course,
> > > $g09root should be meaningful. This command can also be written in
> > > $HOME/.bashrc so that you don't have to type it every time you log in.
> > >
> > > Best regards,
> > > Fuming Ying
> > >
> > >> What's Wrong?>
> > >
> > --
> > Herbert Fruchtl
> > Senior Scientific Computing Officer
>! > School of Chemistry, School of Mathematics and Statistics
> > University of St Andrews
> > --
> > The University of St Andrews is a charity registered in Scotland:
> > No SC013532>
> >
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>

--------------080806030605000505040501-- From owner-chemistry@ccl.net Fri Apr 29 11:00:00 2011 From: "Jean Jules FIFEN julesfifen++gmail.com" To: CCL Subject: CCL: How to install molpro96 on ubuntu? Message-Id: <-44494-110429100105-9120-jF1rObL6Ij9ABn/JpjzIMA|a|server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=0022152d62ad17b0fa04a20f1ad6 Date: Fri, 29 Apr 2011 15:00:52 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen]-[gmail.com] --0022152d62ad17b0fa04a20f1ad6 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL users, Please, would anyone help me about the way to install molpro96 on ubuntu? -- University of Douala Faculty of Science Department of Physics Jean Jules FIFEN --0022152d62ad17b0fa04a20f1ad6 Content-Type: text/html; charset=ISO-8859-1 Dear CCL users,

Please, would anyone help me about the way to install molpro96 on ubuntu?

--
University of Douala
Faculty of Science
Department of Physics

Jean Jules FIFEN


--0022152d62ad17b0fa04a20f1ad6-- From owner-chemistry@ccl.net Fri Apr 29 11:35:01 2011 From: "Marcel Swart marcel.swart * icrea.cat" To: CCL Subject: CCL: implicit solvation Message-Id: <-44495-110429102559-7977-kj4ukyes7vJPH4kXa4d9LQ*|*server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 29 Apr 2011 16:25:40 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Marcel Swart [marcel.swart(-)icrea.cat] Please have a look at: M. A. van Bochove, F. M. Bickelhaupt Nucleophilic Substitution at C, Si and P: How Solvation Affects the Shape of Reaction Profiles Eur. J. Org. Chem. 2008, 649-654 http://www3.interscience.wiley.com/cgi-bin/abstract/117868803/ABSTRACT and you will see that it is not so surprising, if it involves charged species. Much depends on the charge (de)localization in the TS and reactants. Marcel On Apr 29, 2011, at 3:14 PM, Arne Dieckmann adieckma]=[googlemail.com wrote: > Alright, that is what I thought as well. > The energy of transition states of some nucleophilic attacks relative to the energy of the precursors is higher in solution. This is surprising as I anticipated a polar solvent like acetonitrile to lower the energy of these interactions. I would expect stabilizing interactions with any polar solvent for nucleophilic attacks of polar molecules in general. =================================== dr. Marcel Swart ICREA Research Professor at Institut de Química Computacional Universitat de Girona Facultat de Cičncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart[#]icrea.cat marcel.swart[#]udg.edu web http://www.marcelswart.eu =================================== From owner-chemistry@ccl.net Fri Apr 29 12:11:00 2011 From: "Alex M Clark aclark[-]molmatinf.com" To: CCL Subject: CCL: Yield101 app released for iOS Message-Id: <-44496-110429112116-8770-baChLHvtvLK/L7BS2f6aEw,+,server.ccl.net> X-Original-From: "Alex M Clark" Date: Fri, 29 Apr 2011 11:21:12 -0400 Sent to CCL by: "Alex M Clark" [aclark##molmatinf.com] Molecular Materials Informatics and Eidogen-Sertanty have recently co-released another iPhone/iPod/iPad app, called Yield101. This app is a companion to a recent offering - Reaction101 - which was aimed at the education market. Yield101 works with a chemical reaction and allows quantities to be entered for each of the components (e.g. mass, volume, etc.). From the user-entered data, it will calculate the interdependent properties (e.g. mass to moles via molecular weight from structure, mass to volume via density, yield from stoichiometry and molar mass, etc.). The app is designed to be a useful tool for anyone who is running a chemical reaction, starting with students in undergraduate laboratories. It also has a number of additional features, such as preparing (and printing) a nicely formatted PDF document containing the experimental quantities, automatically looking up reactants and products in the Mobile Reagents dataset to check current commercial availability, and sharing of the underlying data with colleagues. For more information, see: http://molmatinf.com/yield101.html http://eidogen-sertanty.com/yield101.html http://itunes.apple.com/us/app/yield101/id433416999 From owner-chemistry@ccl.net Fri Apr 29 13:19:00 2011 From: "Arne Dieckmann adieckma]-[googlemail.com" To: CCL Subject: CCL: implicit solvation Message-Id: <-44497-110429131818-8188-Kk3j8A9mNVWgouhxb/SUVg^^server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 29 Apr 2011 19:18:06 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Arne Dieckmann [adieckma^-^googlemail.com] Great, thanks a lot. That's very helpful. On Apr 29, 2011, at 4:25 PM, Marcel Swart marcel.swart * icrea.cat wrote: > > Sent to CCL by: Marcel Swart [marcel.swart(-)icrea.cat] > > Please have a look at: > > M. A. van Bochove, F. M. Bickelhaupt > Nucleophilic Substitution at C, Si and P: How Solvation Affects the Shape of Reaction Profiles > Eur. J. Org. Chem. 2008, 649-654 > http://www3.interscience.wiley.com/cgi-bin/abstract/117868803/ABSTRACT > > and you will see that it is not so surprising, if it involves charged species. > Much depends on the charge (de)localization in the TS and reactants. > > Marcel > > On Apr 29, 2011, at 3:14 PM, Arne Dieckmann adieckma]=[googlemail.com wrote: > >> Alright, that is what I thought as well. >> The energy of transition states of some nucleophilic attacks relative to the energy of the precursors is higher in solution. This is surprising as I anticipated a polar solvent like acetonitrile to lower the energy of these interactions. I would expect stabilizing interactions with any polar solvent for nucleophilic attacks of polar molecules in general. > > =================================== > dr. Marcel Swart > > ICREA Research Professor at > Institut de Química Computacional > Universitat de Girona > > Facultat de Cičncies > Campus Montilivi > 17071 Girona > Catalunya (Spain) > > tel > +34-972-418861 > fax > +34-972-418356 > e-mail > marcel.swart_-_icrea.cat > marcel.swart_-_udg.edu > web > http://www.marcelswart.eu > ===================================> > From owner-chemistry@ccl.net Fri Apr 29 13:53:01 2011 From: "Kirk Peterson kipeters!A!wsu.edu" To: CCL Subject: CCL: How to install molpro96 on ubuntu? Message-Id: <-44498-110429132617-31108-qb1yJAWj7Rhgb94hGf3L3w() server.ccl.net> X-Original-From: Kirk Peterson Content-Type: multipart/alternative; boundary=Apple-Mail-27--626746751 Date: Fri, 29 Apr 2011 10:26:07 -0700 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Kirk Peterson [kipeters##wsu.edu] --Apple-Mail-27--626746751 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Jean, I would recommend posting this on the molpro users list. regards, Kirk On Apr 29, 2011, at 7:00 AM, Jean Jules FIFEN julesfifen++gmail.com wrote: > Dear CCL users, > > Please, would anyone help me about the way to install molpro96 on ubuntu? > > -- > University of Douala > Faculty of Science > Department of Physics > > Jean Jules FIFEN > > --Apple-Mail-27--626746751 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii Jean,

I would recommend posting this on the molpro users list.

regards,

Kirk

On Apr 29, 2011, at 7:00 AM, Jean Jules FIFEN julesfifen++gmail.com wrote:

Dear CCL users,

Please, would anyone help me about the way to install molpro96 on ubuntu?

--
University of Douala
Faculty of Science
Department of Physics

Jean Jules FIFEN



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