From owner-chemistry@ccl.net Tue May  1 01:32:01 2007
From: "Adam Hunter spacyhunter|a|gmail.com" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL:G: Open-shell singlet
Message-Id: <-34161-070430193202-18888-YXbJnbOmsC5hbBy4FCLfLA,,server.ccl.net>
X-Original-From: Adam Hunter <spacyhunter _ gmail.com>
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Date: Mon, 30 Apr 2007 15:30:48 -0700
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Sent to CCL by: Adam Hunter [spacyhunter:-:gmail.com]
Hi, all,
      I'm new in doing computational chemistry. Now I'm frustrated in 
trying to get the energies of open-shell singlets. Let me study the 
classical O2 example. The 1^Sigma(+) state of the O2 molecule is an 
open-shell singlet. RHF and UHF both can not generate the correct wave 
function b/c the degeneracy of the HOMO and LUMO. So a 
multi-configuration method is needed under such a situation. I've tried 
the CASSCF method but still got a undetermined electronic state. So here 
I want to ask how one can generate the correct wave function for an 
open-shell singlet. By the way, I mainly use the G03 package. If you 
know any other package which can do this job well, I'd like to know also.
     Any help would be greatly appreciated!
best regards
Adam


From owner-chemistry@ccl.net Tue May  1 04:05:00 2007
From: "Jerry Chan chanjcc.:_:.ntu.edu.tw" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: Textbooks for chemical kinetics
Message-Id: <-34162-070501031926-15578-E/2kdxRdWHyZwKi/UaeVRg:_:server.ccl.net>
X-Original-From: Jerry Chan <chanjcc%ntu.edu.tw>
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Date: Tue, 01 May 2007 15:12:31 +0800
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Sent to CCL by: Jerry Chan [chanjcc||ntu.edu.tw]
Dear all,

I am wondering which textbooks are the best for a graduate or senior
undergraduate course on chemical kinetics. In addition to various
reaction mechanisms, the textbook should provide a quantitative
background for the students to understand phenomena such as gas
adsorption on substrate surface, and crystal nucleation and growth process.

Thanks in advance for your suggestion,
Jerry

-- 
Jerry C. C. Chan		phone: 886-2-33662994
Chemistry Department		fax:   886-2-23636359
National Taiwan University
No. 1, Sec. 4, Roosevelt Road
Taipei, Taiwan

http://spin.ch.ntu.edu.tw


From owner-chemistry@ccl.net Tue May  1 06:46:01 2007
From: "Wai-To Chan chan-x-curl.gkcl.yorku.ca" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: Open-shell singlet
Message-Id: <-34163-070501064148-24472-BVMnNctzzPOJs3IIgpT32A^server.ccl.net>
X-Original-From: Wai-To Chan <chan|a|curl.gkcl.yorku.ca>
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Date: Tue, 1 May 2007 07:18:01 -0400 (EDT)
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Sent to CCL by: Wai-To Chan [chan#,#curl.gkcl.yorku.ca]

   Undetermined electronic state for open-shell wave functions is quite common.
I don't think this problem is unique to Gaussian. It also happened to
me often that GAMESS could fail to recognize the state of a UHF or CASSCF 
wavefunction. 

   If the wavefunction is not too far distorted from the 
correct symmetry you may try to determine the electronic state from
inspections of the UHF molecular orbitals or the CASSCF natural 
orbitals. A possible trick which I never tried is to
clean up the MOs by setting infinitesimally small 
numbers to zero and equating nearly equal numbers in the MO coefficients. 

Wai-To Chan


From owner-chemistry@ccl.net Tue May  1 08:30:01 2007
From: "Thomas E Sorensen tes*uwm.edu" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: COLUMBUS Port to GFORTRAN
Message-Id: <-34164-070501082508-23140-RC7buUgoWb+fmXydE5uJ6A%a%server.ccl.net>
X-Original-From: "Thomas E Sorensen" <tes]~[uwm.edu>
Date: Tue, 1 May 2007 08:25:04 -0400


Sent to CCL by: "Thomas E Sorensen" [tes.#%#.uwm.edu]
Has anyone ported COLUMBUS to GFORTRAN? I was hoping to get updated "install.automatic" scripts before I try the port myself.


From owner-chemistry@ccl.net Tue May  1 09:11:00 2007
From: "Frank Neese neese#%#thch.uni-bonn.de" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: Open Shell Singlets
Message-Id: <-34165-070501084853-931-bjC6uj7NpIFy8q5EzADyIw{}server.ccl.net>
X-Original-From: Frank Neese <neese__thch.uni-bonn.de>
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Date: Tue, 01 May 2007 14:48:35 +0200
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Sent to CCL by: Frank Neese [neese++thch.uni-bonn.de]
Dear Adam,

you can do such calculations for example with the ORCA package in the 
ROHF or CASSCF modes. For dynamic correlation either can be followed 
by MRCI or MRPT. You can download the program for free at 
http://www.thch.uni-bonn.de/tc/orca/.

For O2 a reasonable input is:

! ROHF  cc-pVDZ TightSCF

* xyz 0 1
O 0 0 0
O 0 0 1.2
*

The program determines automatically that you look at an open-shell 
singlet state and chooses its options accordingly. The calculations 
gives you one component of the orbitally degenerate 1-Delta state. 
Its energy is -149.56212 Eh. You can do a CASSCF calculation which 
needs 2 electrons in two orbitals. You can either do it for both 
components of the 1-Delta state or you can average of all three 
singlets. A reasonable input is:

!  cc-pVDZ TightSCF

%casscf nel     2
         norb    2
         mult    1
         nroots  2
         end

* xyz 0 1
O 0 0 0
O 0 0 1.2
*

For two roots you get the same energy as in the ROHF case, for three 
roots you get a very slightly higher energy (-149.56210) since the 
orbitals are now a compromise for three singlet states.

You can also average the orbitals over the lowest 3-Sigma and the 
1-Delta state as follows:

!  cc-pVDZ TightSCF

%casscf nel     2
         norb    2
         mult    1,3
         nroots  2,1
         end

* xyz 0 1
O 0 0 0
O 0 0 1.2
*

Finally, introducing dynamic correlation on top of CASSCF may be done 
via MRACPF as follows:

!  cc-pVDZ TightSCF

%casscf nel     2
         norb    2
         mult    1,3
         nroots  2,1
         end

%mrci   citype mracpf
          intmode fulltrafo
         tsel   0
         tpre   1e-4
         newblock 1 *
           nroots 3
           refs cas(2,2) end
           end
         newblock 3 *
           nroots 1
           refs cas(2,2) end
           end
         end

* xyz 0 1
O 0 0 0
O 0 0 1.2
*

The ORCA MRCI program is presently of the "individually selecting" 
type which means that interacting configurations are selected on the 
basis of an estimate for their second order perturbation energy.The 
selection threshold "tsel" is put to zero since this is such a small 
calculation; the result is then "exact".
It is:

-------------------
TRANSITION ENERGIES
-------------------

The lowest energy is   -149.903731790 Eh

State Mult Irrep Root Block    mEh          eV      1/cm
   0    3    -1    0    1      0.000      0.000       0.0
   1    1    -1    1    0     39.078      1.063    8576.7
   2    1    -1    0    0     39.079      1.063    8576.7
   3    1    -1    2    0     57.024      1.552   12515.4

which is very good. With larger basis sets you get it even better.
For larger molecules you need to take tsel on the order of 1e-5 to 
1e-8 and be careful with possible artifacts from the selection. Note 
that such calculations become expensive very quickly.
Many other options are described in the manual of the orca program.

Hope that helps,
all the best,
Frank


From owner-chemistry@ccl.net Tue May  1 11:03:01 2007
From: "John McKelvey jmmckel.:.gmail.com" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: DFT Alphabet Soup Dictionary
Message-Id: <-34166-070501104737-17884-FEyjc+/TggjDV3qDFEtT0Q.:.server.ccl.net>
X-Original-From: "John McKelvey" <jmmckel###gmail.com>
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	boundary="----=_Part_75793_16136969.1178030826981"
Date: Tue, 1 May 2007 10:47:06 -0400
MIME-Version: 1.0


Sent to CCL by: "John McKelvey" [jmmckel!A!gmail.com]
------=_Part_75793_16136969.1178030826981
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Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Folks,

I can't be the only one who could use this, but is there a single, or
perhaps two web sites , or publications that give the functional breakdowns
of the majority of the functionals currently in use?

Best regards,

John McKelvey

------=_Part_75793_16136969.1178030826981
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Folks,<br><br>I can&#39;t be the only one who could use this, but is there a single, or perhaps two web sites , or publications that give the functional breakdowns of the majority of the functionals currently in use?<br><br>
Best regards,<br><br>John McKelvey<br>

------=_Part_75793_16136969.1178030826981--


From owner-chemistry@ccl.net Tue May  1 13:30:01 2007
From: "Wayne Steinmetz WES04747%%pomona.edu" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL: DFT Alphabet Soup Dictionary
Message-Id: <-34167-070501132801-25356-KdzIrYpOt9ShTJchp6vsRw#%#server.ccl.net>
X-Original-From: "Wayne Steinmetz" <WES04747[A]pomona.edu>
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Date: Tue, 1 May 2007 10:27:27 -0700
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Sent to CCL by: "Wayne Steinmetz" [WES04747||pomona.edu]
This is a multi-part message in MIME format.

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You may find the following Web-based review of Perdew's Jacob's Ladder
useful:

http://www-ledss.ujf-grenoble.fr/PERSONNEL/LEDSS7/casida/CompChem/DFT.ht
ml=20

=20

Wayne E. Steinmetz

Carnegie Professor of Chemistry

Woodbadge Course Director

Chemistry Department

Pomona College

645 North College Avenue

Claremont, California 91711-6338

USA

phone: 1-909-621-8447

FAX: 1-909-607-7726

Email: wsteinmetz%pomona.edu

WWW: pages.pomona.edu/~wsteinmetz

=20

________________________________

> From: owner-chemistry%ccl.net [mailto:owner-chemistry%ccl.net]=20
Sent: Tuesday, May 01, 2007 7:47 AM
To: Wayne Steinmetz
Subject: CCL: DFT Alphabet Soup Dictionary

=20

Folks,

I can't be the only one who could use this, but is there a single, or
perhaps two web sites , or publications that give the functional
breakdowns of the majority of the functionals currently in use?

Best regards,

John McKelvey



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<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>You may find the following =
Web-based
review of Perdew&#8217;s Jacob&#8217;s Ladder =
useful:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><a
href=3D"http://www-ledss.ujf-grenoble.fr/PERSONNEL/LEDSS7/casida/CompChem=
/DFT.html">http://www-ledss.ujf-grenoble.fr/PERSONNEL/LEDSS7/casida/CompC=
hem/DFT.html</a>
<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Wayne E. =
Steinmetz</span></font><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Carnegie Professor of =
Chemistry</span></font><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Woodbadge Course =
Director</span></font><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Chemistry =
Department</span></font><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><st1:place w:st=3D"on"><st1:PlaceName =
w:st=3D"on"><font size=3D2
  color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;
  color:navy'>Pomona</span></font></st1:PlaceName><font size=3D2 =
color=3Dnavy
 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;color:navy'> <st1:PlaceType
 w:st=3D"on">College</st1:PlaceType></span></font></st1:place><font =
color=3Dnavy><span
style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><st1:Street w:st=3D"on"><st1:address =
w:st=3D"on"><font size=3D2
  color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;
  color:navy'>645 North College =
Avenue</span></font></st1:address></st1:Street><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><st1:place w:st=3D"on"><st1:City w:st=3D"on"><font =
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  color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;
  color:navy'>Claremont</span></font></st1:City><font size=3D2 =
color=3Dnavy
 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;color:navy'>, <st1:State
 w:st=3D"on">California</st1:State> <st1:PostalCode =
w:st=3D"on">91711-6338</st1:PostalCode></span></font></st1:place><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><st1:country-region w:st=3D"on"><st1:place =
w:st=3D"on"><font
  size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;
  color:navy'>USA</span></font></st1:place></st1:country-region><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>phone: =
1-909-621-8447</span></font><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>FAX: =
1-909-607-7726</span></font><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Email: =
wsteinmetz%pomona.edu</span></font><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>WWW: =
pages.pomona.edu/~wsteinmetz</span></font><font
color=3Dnavy><span style=3D'color:navy'><o:p></o:p></span></font></p>

</div>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<div>

<div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><font =
size=3D3
face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>

<hr size=3D2 width=3D"100%" align=3Dcenter tabindex=3D-1>

</span></font></div>

<p class=3DMsoNormal><b><font size=3D2 face=3DTahoma><span =
style=3D'font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font =
size=3D2
face=3DTahoma><span style=3D'font-size:10.0pt;font-family:Tahoma'>
owner-chemistry%ccl.net [mailto:owner-chemistry%ccl.net] <br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> Tuesday, May 01, =
2007 7:47
AM<br>
<b><span style=3D'font-weight:bold'>To:</span></b> <st1:PersonName =
w:st=3D"on">Wayne
 Steinmetz</st1:PersonName><br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> CCL: DFT =
Alphabet Soup
Dictionary</span></font><o:p></o:p></p>

</div>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Folks,<br>
<br>
I can't be the only one who could use this, but is there a single, or =
perhaps
two web sites , or publications that give the functional breakdowns of =
the
majority of the functionals currently in use?<br>
<br>
Best regards,<br>
<br>
John McKelvey<o:p></o:p></span></font></p>

</div>

</body>

</html>

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From owner-chemistry@ccl.net Tue May  1 14:04:00 2007
From: "Atul Agarwal aagarwal###achillion.com" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: amine prodrugs
Message-Id: <-34168-070501104253-17407-anyacX30wX9BVcu1ODuwWA|,|server.ccl.net>
X-Original-From: "Atul  Agarwal" <aagarwal~~achillion.com>
Date: Tue, 1 May 2007 10:42:50 -0400


Sent to CCL by: "Atul  Agarwal" [aagarwal-$-achillion.com]
Fellow Comp chemists,

Has anyone done any calculations on phosphate prodrugs of amines?  There are two steps involved in the release of parent, bio-conversion (hydrolysis) of the phosphate to yield (e.g.) hydroxymethoxycarbonyl linker, and subsequently, cleavage of amino acid ester through intramolecular nucleophilic catalysis.  I am looking for ways to predict the rates of these two steps.  An example of such prodrugs can be found in the following ref (Bioorg Med Chem Lett 10, 2000, 1121).

I would appreciate any clues.

thanks,
Atul

Atul Agarwal
Achillion Pharm
300 George St
New Haven, CT  06511
aagarwal++achillion.com


From owner-chemistry@ccl.net Tue May  1 14:39:01 2007
From: "Alexandr Isayev alex|a|ccmsi.us" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: DFT Alphabet Soup Dictionary
Message-Id: <-34169-070501141952-24813-ocJHkatGDOQhb0/7z2zEGA(0)server.ccl.net>
X-Original-From: Alexandr Isayev <alex^-^ccmsi.us>
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Date: Tue, 1 May 2007 12:43:27 -0500
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Sent to CCL by: Alexandr Isayev [alex]_[ccmsi.us]
Hi John,

There is nice introductorily book on DFT "A Chemist's Guide to Density
Functional Theory"
http://www.amazon.com/Chemists-Guide-Density-Functional-Theory/dp/3527303723

Sincerely,
Alexandr

Tuesday, May 1, 2007, 9:47:06 AM, you wrote:

JMjgc> Folks,

JMjgc> I can't be the only one who could use this, but is there a
JMjgc> single, or perhaps two web sites , or publications that give
JMjgc> the functional breakdowns of the majority of the functionals currently in use?

JMjgc>  Best regards,

JMjgc> John McKelvey
JMjgc>   


-------------------------------------------------------
Alexandr Isayev,
Graduate Research Assistant, and System Administrator
\a/ Computational Center for Molecular Structure
and Interactions (CCMSI),
Jackson State University,
Jackson, MS USA
   Tel:  +(601) 979-1134
e-mail:  alex(at)ccmsi.us
   Web:  http://www.ccmsi.us
--------------------------------------------------------


From owner-chemistry@ccl.net Tue May  1 22:14:01 2007
From: "Senthil Natesan sen.natesan]=[yahoo.com" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: computing cross sectional area of a molecule
Message-Id: <-34170-070501153127-9648-cJ33iu7WORPfWEq0nbDjDQ:-:server.ccl.net>
X-Original-From: "Senthil  Natesan" <sen.natesan%yahoo.com>
Date: Tue, 1 May 2007 15:31:24 -0400


Sent to CCL by: "Senthil  Natesan" [sen.natesan|-|yahoo.com]

Dear Colleagues,

Can anyone suggest me a program or method to compute cross sectional area of a given molecule?..

Thanks in advance..

Senthil Natesan


From owner-chemistry@ccl.net Tue May  1 22:49:01 2007
From: "Andrej Grubisic agrubisic-,-jhu.edu" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Textbooks for chemical kinetics
Message-Id: <-34171-070501120508-16727-kdWw+u8xlPskR7i+9T8E0g^^server.ccl.net>
X-Original-From: "Andrej Grubisic" <agrubisic+*+jhu.edu>
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Date: Tue, 1 May 2007 11:01:37 -0400
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Sent to CCL by: "Andrej Grubisic" [agrubisic * jhu.edu]
Dear Jerry,

I've used the following textbook and found it very useful for kinetics
problems:
Chemical Kinetics and Reaction Dynamics by Paul L. Houston 
     ISBN:  0072435372  (McGraw-Hill Science/Engineering/Math, 2001-03-22)
It is a great book for introducing kinetics through phenomenological
standpoint as well as for advanced level from underlying quantum theory. I
don't remember coming across crystal nucleation and growth processes in it,
though.

Hope it helps
Andrej


-----Original Message-----
> From: owner-chemistry===ccl.net [mailto:owner-chemistry===ccl.net] 
Sent: Tuesday, May 01, 2007 3:13 AM
To: Grubisic, Andrej 
Subject: CCL: Textbooks for chemical kinetics


Sent to CCL by: Jerry Chan [chanjcc||ntu.edu.tw]
Dear all,

I am wondering which textbooks are the best for a graduate or senior
undergraduate course on chemical kinetics. In addition to various
reaction mechanisms, the textbook should provide a quantitative
background for the students to understand phenomena such as gas
adsorption on substrate surface, and crystal nucleation and growth process.

Thanks in advance for your suggestion,
Jerry

-- 
Jerry C. C. Chan		phone: 886-2-33662994
Chemistry Department		fax:   886-2-23636359
National Taiwan University
No. 1, Sec. 4, Roosevelt Road
Taipei, Taiwan

http://spin.ch.ntu.edu.twhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt