From owner-chemistry@ccl.net Thu Mar  2 01:14:00 2006
From: "Charles McCallum mmccallum**pacific.edu" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: MD stability criterion
Message-Id: <-31081-060301232155-13810-+m1ecpn6xlSAAH9JpGHqwA-,-server.ccl.net>
X-Original-From: Charles McCallum <mmccallum,,pacific.edu>
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Sent to CCL by: Charles McCallum [mmccallum-*-pacific.edu]

Hi Anselm,

<E> is always the canonical mean;  in other words, you can't do these  
calculations "on the fly", you must run your whole trajectory, then  
go back and find the fluctuations....

Hope this helps,

Mike

On Mar 1, 2006, at 7:31 AM, Anselm H C Horn Anselm.Horn{:}chemie.uni- 
erlangen.de wrote:

> Sent to CCL by: "Anselm  H C Horn" [Anselm.Horn:+:chemie.uni- 
> erlangen.de]
> Dear all,
>
> I have a (probably rather simple) question regarding a well-known  
> stability criterion in molecular dynamics simulations: The decimal  
> logarithm of the ratio between the average fluctuation of the total  
> energy <Delta E> and the average total energy <E> is calculated  
> according to
> log_10 ( <Delta_E> / <E> ) =
> log_10 ( < E(t) - <E> > / <E> )
> (cf Becker & Karplus, Springer 2006)
>
> When one calculates this value for a certain time t of a completed  
> MD trajectory, is <E> then the mean energy of the complete  
> trajectory or just up to the snapshot of time frame t?
>
> Many thanks in advance.
>
> Best regards,
>
> Anselm
>
> Computer Chemie Centrum
> Friedrich-Alexander-Universitaet Erlangen-Nuernberg
> Germany
>
>
>
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>

--
C. Michael McCallum           http://www.pacific.edu/college/ 
chemistry/McCallum/cmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  /  
(209) 946-2607 fax


From owner-chemistry@ccl.net Thu Mar  2 02:53:01 2006
From: "nokophala_-_aim.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL:G: LANL2DZ vs SDD
Message-Id: <-31082-060228094555-16556-vL31YAvN8dGXH07XH4ohFg*_*server.ccl.net>
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Sent to CCL by: nokophala*_*aim.com



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At lest for LanL2DZ the relativistic effects are 'averaged out' in the ECP, LanL. Always better to check though, by e.g. calculating IPs of the atoms of interest. LanL2DZ always gave me results that are sometimes better than all elect calcs with scalar relativistic corrections. For clusters, however, the metal-metal bond distances are over estimated and scalar relativistic calcs might be better.
 
 
Dr Noko Phala
Principal Metallurgist
Technology Department
Anglo Research 
PO Box 106 Crown Mines 2025
Republic of South Africa
Tel: +27 (11) 377 4817
e-mail: nphala[-]angloresearch.com 

 
-----Original Message-----
> From: Joslyn Y Kravitz jyudenfr-x-umich.edu <owner-chemistry[-]ccl.net>
To: Phala, Noko  <nokophala[-]aim.com>
Sent: Mon, 27 Feb 2006 12:31:14 -0500
Subject: CCL:G: LANL2DZ vs SDD


Sent to CCL by: Joslyn Y Kravitz [jyudenfr ~ umich.edu]
SDD is a triple zeta basis set and LanL2DZ is a double zeta basis set, 
which is likely why the SDD is better. I am not sure of the difference in 
how they treat relativistic effects.

Joslyn Kravitz



On Sun, 26 Feb 2006, zjwu zjwu a imr.edu wrote:

> Sent to CCL by: "zjwu" [zjwu#imr.edu]
> Hi, all,
>
> I have maybe a naive question about the basis sets LANL2DZ and SDD which are 
the standard basis sets in Gaussian package. I am now using the two basis sets 
to calculate the systems containing 4d and 5d elements (including rare earth 
elements).My question is:
>
> What is the difference of the two basis sets in dealing with relativistic 
effects and spin-orbit coupling effect?
>
> The two basis sets use the same valence electrons for 4d and 5d elements, but 
it seems SDD is better than LANL2DZ.
>
> Thank you very much.
>
> Zhijian WUhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________________________________________________
Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection.

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<HTML><BODY><DIV style='font-family: "Verdana"; font-size: 10pt;'><DIV>
<DIV>At lest for LanL2DZ the relativistic effects are 'averaged out' in the ECP, LanL. Always better to check though, by e.g. calculating IPs of the atoms of interest.&nbsp;LanL2DZ always gave me results that are sometimes better than&nbsp;all elect calcs with scalar relativistic corrections. For clusters, however, the metal-metal bond distances are over estimated and scalar relativistic calcs might be better.</DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'; mso-no-proof: yes">Dr Noko Phala</SPAN><SPAN style="mso-no-proof: yes"><?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'; mso-no-proof: yes">Principal Metallurgist</SPAN><SPAN style="mso-no-proof: yes"><o:p></o:p></SPAN></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'; mso-no-proof: yes">Technology Department</SPAN><SPAN style="mso-no-proof: yes"><o:p></o:p></SPAN></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'; mso-no-proof: yes">Anglo Research </SPAN><SPAN style="mso-no-proof: yes"><o:p></o:p></SPAN></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'; mso-no-proof: yes">PO Box 106 Crown Mines 2025</SPAN><SPAN style="mso-no-proof: yes"><o:p></o:p></SPAN></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'; mso-no-proof: yes">Republic of South Africa</SPAN><SPAN style="mso-no-proof: yes"><o:p></o:p></SPAN></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'; mso-no-proof: yes">Tel: +27 (11) 377 4817</SPAN><SPAN style="mso-no-proof: yes"><o:p></o:p></SPAN></DIV>
<DIV class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'; mso-no-proof: yes">e-mail: </SPAN><SPAN style="mso-no-proof: yes"><A href="mailto:nphala[-]angloresearch.com"><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'">nphala[-]angloresearch.com</SPAN></A></SPAN><SPAN style="FONT-SIZE: 10pt; COLOR: gray; FONT-FAMILY: 'Comic Sans MS'; mso-no-proof: yes"> </SPAN><o:p></o:p></DIV><BR>&nbsp;<BR>-----Original Message-----<BR>From: Joslyn Y Kravitz jyudenfr-x-umich.edu &lt;owner-chemistry[-]ccl.net&gt;<BR>To: Phala, Noko  &lt;nokophala[-]aim.com&gt;<BR>Sent: Mon, 27 Feb 2006 12:31:14 -0500<BR>Subject: CCL:G: LANL2DZ vs SDD<BR><BR>
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<DIV class=AOLPlainTextBody id=AOLMsgPart_0_07afa8a1-ace9-4a28-bc3f-13a2203e4e49><PRE><TT>Sent to CCL by: Joslyn Y Kravitz [jyudenfr ~ umich.edu]
SDD is a triple zeta basis set and LanL2DZ is a double zeta basis set, 
which is likely why the SDD is better. I am not sure of the difference in 
how they treat relativistic effects.

Joslyn Kravitz



On Sun, 26 Feb 2006, zjwu zjwu a imr.edu wrote:

&gt; Sent to CCL by: "zjwu" [zjwu#imr.edu]
&gt; Hi, all,
&gt;
&gt; I have maybe a naive question about the basis sets LANL2DZ and SDD which are 
the standard basis sets in Gaussian package. I am now using the two basis sets 
to calculate the systems containing 4d and 5d elements (including rare earth 
elements).My question is:
&gt;
&gt; What is the difference of the two basis sets in dealing with relativistic 
effects and spin-orbit coupling effect?
&gt;
&gt; The two basis sets use the same valence electrons for 4d and 5d elements, but 
it seems SDD is better than LANL2DZ.
&gt;
&gt; Thank you very much.
&gt;
&gt; Zhijian WU&gt;
&gt;
&gt;
&gt;
&gt;
&gt;E-mail to subscribers: <A href="mailto:CHEMISTRY%40ccl.net">CHEMISTRY[-]ccl.net</A> or use:
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From owner-chemistry@ccl.net Thu Mar  2 05:57:00 2006
From: "Mariusz Radon mariusz.radon|gmail.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL:G: problem with PCM in g03
Message-Id: <-31083-060302055524-4358-xjUqeC0xr8vFPkBEAFwdpg%%server.ccl.net>
X-Original-From: "Mariusz Radon" <mariusz.radon!=!gmail.com>
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Date: Thu, 2 Mar 2006 11:55:19 +0100
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Sent to CCL by: "Mariusz Radon" [mariusz.radon]~[gmail.com]
Dear CCLers,

Some time ago I reported a problem with PCM model in Gaussian 03. It
seems some other people had it also, so I forward the solution I've
received from gaussian help center. It seems working fine!

Take care,
Mariusz

---------- Forwarded message ----------
> From: help() gaussian.com <help() gaussian.com>
Date: Feb 28, 2006 8:35 PM
Subject: Re: CCL:G: problem with PCM in g03
To: mariusz.radon() gmail.com

  Dr. Radon,

    this is an issue with building the cavity and while symmetry was
sometimes a fix in the past it is better to start by tweaking the
cavity generation parameters a little.  One set which has been tested
internally is to use

#  .. SCRF=(PCM,Read) ...

and then in the PCM input section after the structure

OFac=0.8  RMin=0.5

which gives you a slightly rougher cavity, fewer small spheres, but still
adequate for good energy and gradients.


From owner-chemistry@ccl.net Thu Mar  2 07:44:00 2006
From: "Pablo Vitoria pablo.vitoria^^^ehu.es" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL:G: RI DFT approximation in G03
Message-Id: <-31084-060302073747-4186-Ro5g4j9SkwqoMAa1VVtstg_+_server.ccl.net>
X-Original-From: "Pablo Vitoria" <pablo.vitoria!=!ehu.es>
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Date: Thu, 2 Mar 2006 13:37:31 +0100
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Sent to CCL by: "Pablo Vitoria" [pablo.vitoria(!)ehu.es]
Hi,

Since my DFT calculations are getting bigger and bigger, I decided to try 
using auxiliary basis sets to fit the Coulomb energy (RI aprox) in Gaussian 
03, using the very recently published Coulomb-fitting basis sets of F. 
Weigend (PCCP, 2006, 8, 1057) together with the new Ahlrichs def2 basis 
(PCCP, 2005, 7, 3297).

To my surprise, I found big total energy differences between RI and non-RI 
calculations in some test calculations. For example, for acetone [BP86 
functional, SV(P) basis], the difference is 73 miliHartree, a thousand times 
the one quoted in the PCCP paper, about 90 microH. The same happes with WO 
(61 miliH) and other molecules.

As I do not have access to Turbomole, which is the software these bases were 
developed for, I ran the calculations again using ORCA 2.4.45 to check the 
results. For acetone (exactly same geometry and basis), the difference in 
energy between the RI and non-RI calculation turns out to be the expected 90 
microH.
Besides, using ORCA to optimize the geometry, both calculations give almost 
exactly the same result (difference is 0.0001 A and 0.01 degree), whereas in 
G03 the geometries are very different using RI (0.05 A, 0.6 degree).

This is the first time I use Coulomb-fitting basis sets with any software, 
and I would be very grateful if someone more experienced could help me with 
this. Below you can find the Gaussian 03 input file.

Thank you very much
Best regards

Pablo

#P BP86/Gen/Gen scf=tight opt freq

H2CO RI

0 1
C
O 1  1.2029
H 1  1.1075 2 122.016
H 1  1.1075 2 122.016 3 180.00

H 0
   s  3
 13.010701000      0.19682158000E-01
 1.9622572000      0.13796524000
 0.44453796000      0.47831935000
   s  1
 0.12194962000       1.0000000000
****
C 0
   s  5
 1238.4016938      0.54568832082E-02
 186.29004992      0.40638409211E-01
 42.251176346      0.18025593888
 11.676557932      0.46315121755
 3.5930506482      0.44087173314
   s  1
 0.40245147363       1.0000000000
   s  1
 0.13090182668       1.0000000000
   p  3
 9.4680970621      0.38387871728E-01
 2.0103545142      0.21117025112
 0.54771004707      0.51328172114
   p  1
 0.15268613795       1.0000000000
   d  1
 0.80000000000       1.0000000000
****
O 0
   s  5
 2266.1767785     -0.53431809926E-02
 340.87010191     -0.39890039230E-01
 77.363135167     -0.17853911985
 21.479644940     -0.46427684959
 6.6589433124     -0.44309745172
   s  1
 0.80975975668       1.0000000000
   s  1
 0.25530772234       1.0000000000
   p  3
 17.721504317      0.43394573193E-01
 3.8635505440      0.23094120765
 1.0480920883      0.51375311064
   p  1
 0.27641544411       1.0000000000
   d  1
 1.2000000000       1.0000000000
****

H 0
s  3
 15.6752927 0.0186886
 3.6063578 0.0631670
 1.2080016 0.1204609
s  1
 0.4726794 0.0592485
s  1
 0.2018100 0.0051272
p  2
 2.0281365 1.0
 0.5358730 1.0
d  1
 2.2165124 0.0033116
****
C 0
s  7
 1861.0916331 0.0744171
 642.9939764 0.1653957
 235.1105725 0.5576484
 90.7028894 1.3108298
 36.7794552 2.1694681
 15.6046273 1.7668846
 6.8907294 0.2930769
s  1
 3.1478850 -0.1708702
s  1
 1.4777287 0.1641553
s  1
 0.7076466 0.4149941
s  1
 0.3430122 0.1624366
s  1
 0.1669453 0.0207675
p  2
 13.5472892 -0.0206477
 5.4669419 -0.0115282
p  1
 2.1751721 0.0455914
p  1
 0.8582194 0.0028360
p  1
 0.3376720 0.0181875
d  2
 5.9287253 -0.0225948
 1.9809209 -0.0476827
d  1
 0.8055417 -0.0365372
d  1
 0.3531244 -0.0145417
f  2
 1.6755626 0.0088798
 0.5997536 0.0069903
g  1
 1.0024600 -0.0022192
****
O 0
s  7
 2876.8216605 0.1443558
 1004.7443032 0.2920041
 369.7579954 1.0258517
 142.9442404 2.2875516
 57.8366425 3.6080237
 24.3864983 2.3737865
 10.6622662 0.0489414
s  1
 4.8070437 -0.1295186
s  1
 2.2210770 0.7747158
s  1
 1.0447795 0.7647816
s  1
 0.4968425 0.2369803
s  1
 0.2371384 0.0208099
p  2
 64.2613382 -0.0126659
 16.3006076 -0.0378744
p  1
 4.3550542 0.0638078
p  1
 1.2019554 0.0169516
p  1
 0.3354196 0.0065743
d  2
 9.2146611 -0.0597914
 2.8435251 -0.0846724
d  1
 0.9955759 -0.0466066
d  1
 0.3649441 -0.0096978
f  2
 2.6420115 1.0
 0.7345613 1.0
g  1
 1.3931000 -0.0016533
****


-----------------------------------
Pablo Vitoria Garcia
Dpto. Química Inorgánica, Fac. Ciencias
Universidad del País Vasco (UPV/EHU)
P.O. Box 644
E-48080 Bilbao (Bizkaia) SPAIN

Phone: +34 946015992
Fax: +34 946013500


From owner-chemistry@ccl.net Thu Mar  2 08:49:00 2006
From: "Senthil Kumar Natesan senthilkumar_natesan .. bi.iiita.ac.in" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: DOCK(grid) input files
Message-Id: <-31085-060302021228-16581-GIGYuCzkC9DeCGTO9S4Nrw-#-server.ccl.net>
X-Original-From: "Senthil Kumar  Natesan" <senthilkumar_natesan:_:bi.iiita.ac.in>
Date: Thu, 2 Mar 2006 02:12:27 -0500


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 Thu Mar  2 11:54:00 2006
From: "Martin Korth mkorth[A]muenster.de" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: QMC__HOME - a QMC public ressource computing project
Message-Id: <-31086-060302091349-17036-85r0OIhW4KZ7sC5L52weEQ__server.ccl.net>
X-Original-From: Martin Korth <mkorth\a/muenster.de>
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Date: Thu, 2 Mar 2006 14:13:38 +0100
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Sent to CCL by: Martin Korth [mkorth]^[muenster.de]
Dear CCL'ers,

hereby we announce the public release of the first
chemistry public ressource computing project
"Quantum Monte Carlo at Home".
Details can be found on the Internet:
http://qah.uni-muenster.de

One of the major advantages of QMC for electronic structure calculations is 
the ability to perform massive parallel calculations. This can be utilized to 
distribute work over hundreds or even thousands of processors. In our project 
we make use of this advantage to raise computing time with the help of 
volunteers all over the world. 

Taking part is simple:
1. Visit our website http://qah.uni-muenster.de
2. Download and install the client software
3. Donate CPU time for research into QMC
(works quite similar to a screensaver)

QMC#%#HOME makes use of
the QMC program Amolqc by Lüchow et al
http://www.ipc.rwth-aachen.de/luechow/
and the BOINC PRC middleware  
http://boinc.berkeley.edu/
and is funded by the Sonderforschungsbereich 424
'Molecular Orientation and its Functions in Chemical Systems'
established by the Deutsche Forschungsgemeinschaft
http://www.uni-muenster.de/Chemie.oc/sfb.html

Best regards,
Martin Korth
Ph.D. student

Prof. Stefan Grimme
Molecular Quantum Chemistry
University of Münster
Germany


From owner-chemistry@ccl.net Thu Mar  2 12:29:02 2006
From: "omar Deeb deeb2000il ~~ yahoo.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: Parameters for Gold
Message-Id: <-31087-060302121127-29376-jDoL6u4JXUPbRQxHQPLubw++server.ccl.net>
X-Original-From: omar Deeb <deeb2000il%x%yahoo.com>
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Date: Thu, 2 Mar 2006 09:11:22 -0800 (PST)
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Sent to CCL by: omar Deeb [deeb2000il~~yahoo.com]
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Dear CCl,
  I am searching for a semiepirical method that has  parameters for gold (Au).
  Thanks in advance.
   
   
   


Dr. Omar Deeb 
Assistant Professor , PhD
Theoretical/computational chemist
Chemistry and chemical technology department
Faculty of science and technology
Alquds University
Abu-deis, Jerusalem
e-mail : deeb2000il()yahoo.com
		
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Yahoo! Mail
Bring photos to life! New PhotoMail  makes sharing a breeze. 
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<div>Dear CCl,</div>  <div>I am searching for a semiepirical method that has&nbsp; parameters for gold (Au).</div>  <div>Thanks in advance.</div>  <div>&nbsp;</div>  <div>&nbsp;</div>  <div>&nbsp;</div><BR><BR>Dr. Omar Deeb <br>Assistant Professor , PhD<br>Theoretical/computational chemist<br>Chemistry and chemical technology department<br>Faculty of science and technology<br>Alquds University<br>Abu-deis, Jerusalem<br>e-mail : deeb2000il()yahoo.com<p>
		<hr size=1>Yahoo! Mail<br>
Bring photos to life! <a href="http://pa.yahoo.com/*http://us.rd.yahoo.com/evt=39174/*http://photomail.mail.yahoo.com">New PhotoMail </a> makes sharing a breeze. 

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From owner-chemistry@ccl.net Thu Mar  2 13:49:00 2006
From: "Elaine Meng meng~!~cgl.ucsf.edu" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: DOCK(grid) input files
Message-Id: <-31088-060302134640-7928-fRfvDcYivai6ntHibP+3VA,server.ccl.net>
X-Original-From: Elaine Meng <meng/./cgl.ucsf.edu>
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Sent to CCL by: Elaine Meng [meng-.-cgl.ucsf.edu]
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 Thu Mar  2 19:34:00 2006
From: "Gonzalo Jimenez Oses gonzalo.jimenez[#]dq.unirioja.es" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: Thermodynamic reversibility criterion
Message-Id: <-31089-060302190922-9336-T2oqLpsbNMuVc4YmdpxDGw ~ server.ccl.net>
X-Original-From: "Gonzalo Jimenez Oses" <gonzalo.jimenez^-^dq.unirioja.es>
Date: Thu, 2 Mar 2006 19:09:21 -0500


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


From owner-chemistry@ccl.net Thu Mar  2 21:45:00 2006
From: "Dr. Seth Olsen s.olsen1%uq.edu.au" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: Thermodynamic reversibility criterion
Message-Id: <-31090-060302205510-8658-VhHFY1DZjbVXN/y0zzwM2A~~server.ccl.net>
X-Original-From: "Dr. Seth Olsen" <s.olsen1=uq.edu.au>
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Date: Fri, 03 Mar 2006 11:54:59 +1000
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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>
>
>
>  
>


-- 
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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


From owner-chemistry@ccl.net Thu Mar  2 23:34:00 2006
From: "Roel Sigifredo Sanchez-Carrera roel * gatech.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: Phonon Spectra of Organic Molecular Crystals
Message-Id: <-31091-060302224243-9194-qqY0Umpk3TcOlkChLG/bwg---server.ccl.net>
X-Original-From: "Roel Sigifredo Sanchez-Carrera" <roel_._gatech.edu>
Date: Thu, 2 Mar 2006 22:42:40 -0500


Sent to CCL by: "Roel Sigifredo Sanchez-Carrera" [roel _ gatech.edu]
Dear CCL members,

I would like to know if there is any computational software (commercial or non-commercial) that will allow me to compute the phonon spectra of organic molecular crystals at either semiempirical, ab initio or DFT level.

In advance thanks for your response.

Sigifredo Sanchez-Carrera
roel ~ gatech.edu
Georgia Institute of Technology
770 State Street
Atlanta, GA 30332-0400