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Date: Tue, 2 Mar 1999 16:16:51 +1100
From: Bill King <Bill.King@anu.edu.au>
To: CHEMISTRY@www.ccl.net
Subject: Intrinsic C13 Isotope Effects for Decarboxylations
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Dear CCLers,

Could anyone provide me with a (or some) recent reference(s) that gives the 
range of intrinsic carbon isotope effects in decarboxylation reactions. I am 
most interested in beta-keto acids, but any general information would be 
useful.

Thanks in advance
Bill

---
Bill King                                     | email: Bill.King@anu.edu.au 
Division of Biochemistry and Molecular Biology| 
John Curtin School of Medical Research        | phone: +61-2-6279-8303       
PO Box 334 Canberra ACT 2601                  | FAX:   +61-2-6249-0415          

From chemistry-request@www.ccl.net  Tue Mar  2 04:23:44 1999
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From: Harald Svedung <svedung@phc.chalmers.se>
To: Anatoli Korkin <r40757@email.mot.com>
cc: CCL <chemistry@www.ccl.net>
Subject: Re: CCL:Lennard-Jones Parameters
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Hi Anatoli,

Have a look at the following papers:

T. A. Hallgren, J. Am. Chem. Soc. 114 (1992) 7827.
S. J. Weiner, P. A. Kollman, D. T. Nguyen, D. A. Case, J. Comp. Chem. 7 
(1986) 230.

Be aware that L-J potentials are generally quite hard in the repulsive 
region. We will in our next paper state that there is a need for 
systematic studies of hardness of interaction between atoms or molecules.
In some applications, e.g. collisional energy transfer, interaction 
steepness is important.

all the best
:-)
/Harald


On Mon, 1 Mar 1999, Anatoli Korkin wrote:

> Dear Colleagues,
> 
> 
> Sorry, it is probably a text book question. Does anyone knows a good 
> complilation of Lennard-Jones parameters, delta and epsilon, and 
> paper(s)/review(s) of methods of their calculations. 
> 
> Thank you,
> 
> Anatoli Korkin
> 
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Harald Svedung (M.Sc.)                  phone:          +46-31-7722816
Department of Chemistry                 fax:            +46-31-167194
Physical Chemistry                      home phone:     +46-31-240897, +46-709223206	
Goeteborg University                    home e-mail:    harald.svedung@svedung.pp.se
SE-412 96 Goeteborg, Sweden             www.che.chalmers.se/~svedung/	


From chemistry-request@www.ccl.net  Tue Mar  2 09:35:39 1999
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All,

I know this has been asked before, but I was unable to find a useful
response in the archives:

Are the IGLO basis sets (specifically sets II and III) available on the
web or in an electronic form?

On a related note are the "complete" set of Huzinaga basis sets (for
example those from the book "Gaussian Basis Sets for Molecular
Calculations" or from some of his early papers like Approx. Atomic
Functions from 1971)?  I've ordered this book, but need it faster than
4-6 weeks.

Thanks, Bill

--
************************************************************************
*    "Like jewels in a crown, the precious stones glittered in the     *
*     queen's round metal hat." - Jack Handey                          *
*                                                                      *
*     Bill Laidig                                                      *
*     The Procter & Gamble Co.             tel 513-627-2857 fax - 1233 *
*     Miami Valley Laboratories            laidig@pg.com (preferred)   *
*     P.O. Box 538707                      laidig.wd@pg.com            *
*     Cincinnati, OH 45253-8707                                        *
************************************************************************




From chemistry-request@www.ccl.net  Tue Mar  2 10:08:47 1999
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Bill

Here are a few references that might be useful.  Also, there probably is
an article or two in Methods in Enzymology.

Swanson T, Brooks HB, Osterman AL, O'Leary MH, Phillips MA Biochemistry
1998 37(42):14943-7

Schimerlik, M.I., Rife, J.E., and Cleland, W.W. (1975), Biochemistry 14,
5347

Hermes, J. D., Roeske, C. A., O'Leary, M. H., & Cleland, W. W. (1982)
Biochemistry 21, 5106-5114

Edens WA, Urbauer JL, Cleland WW Biochemistry 1997 36(5):1141-7 

Urbauer JL, Bradshaw DE, Cleland WW Biochemistry 1998 37(51):18026-31

On Tue, 2 Mar 1999, Bill King wrote:

> 
> Dear CCLers,
> 
> Could anyone provide me with a (or some) recent reference(s) that gives the 
> range of intrinsic carbon isotope effects in decarboxylation reactions. I am 
> most interested in beta-keto acids, but any general information would be 
> useful.
> 
> Thanks in advance
> Bill
> 
> ---
> Bill King                                     | email: Bill.King@anu.edu.au 
> Division of Biochemistry and Molecular Biology| 
> John Curtin School of Medical Research        | phone: +61-2-6279-8303       
> PO Box 334 Canberra ACT 2601                  | FAX:   +61-2-6249-0415          


From chemistry-request@www.ccl.net  Tue Mar  2 11:49:46 1999
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> Dear CCL'ers,
> 
> 	is anybody aware of a software package that has a conformational
> search tool applicable to ring-systems ?
> 
> Regards,
> 
> Christian
> 
Dear Christian,

If you mean on "conformational search tool applicable to 
ring-systems" the calculation of ring-puckering data,
distances from least-square planes, torsional angles in rings,
different pyramidality indices of atoms, 
then have a look on Mol2mol at

www.compuchem.com/mol2mol.htm

best regards

Tamas


************************************************************************
   Dr Tamas E. Gunda                   phone: (+36-52) 316666-2479
   Research Group of Antibiotics       fax  : (+36-52) 310936
   L. Kossuth University               e-mail: tamasgunda@tigris.klte.hu
   POBox 36                            http://www.klte.hu/~gundat               
   H-4010 Debrecen
   Hungary
************************************************************************

From chemistry-request@www.ccl.net  Tue Mar  2 11:55:43 1999
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> Dear CCL'ers,
> 
> 	is anybody aware of a software package that has a conformational
> search tool applicable to ring-systems ?
> 
> Regards,
> 
> Christian
> 
Dear Christian,

If you mean on "conformational search tool applicable to 
ring-systems" the calculation of ring-puckering data,
distances from least-square planes, torsional angles in rings,
different pyramidality indices of atoms, 
then have a look on Mol2mol at

www.compuchem.com/mol2mol.htm

best regards

Tamas


************************************************************************
   Dr Tamas E. Gunda                   phone: (+36-52) 316666-2479
   Research Group of Antibiotics       fax  : (+36-52) 310936
   L. Kossuth University               e-mail: tamasgunda@tigris.klte.hu
   POBox 36                            http://www.klte.hu/~gundat               
   H-4010 Debrecen
   Hungary
************************************************************************

From chemistry-request@www.ccl.net  Tue Mar  2 11:56:35 1999
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> Dear CCL'ers,
> 
> 	is anybody aware of a software package that has a conformational
> search tool applicable to ring-systems ?
> 
> Regards,
> 
> Christian
> 
Dear Christian,

If you mean on "conformational search tool applicable to 
ring-systems" the calculation of ring-puckering data,
distances from least-square planes, torsional angles in rings,
different pyramidality indices of atoms, 
then have a look on Mol2mol at

www.compuchem.com/mol2mol.htm

best regards

Tamas


************************************************************************
   Dr Tamas E. Gunda                   phone: (+36-52) 316666-2479
   Research Group of Antibiotics       fax  : (+36-52) 310936
   L. Kossuth University               e-mail: tamasgunda@tigris.klte.hu
   POBox 36                            http://www.klte.hu/~gundat               
   H-4010 Debrecen
   Hungary
************************************************************************

From chemistry-request@www.ccl.net  Mon Mar  1 04:25:05 1999
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From: Jochen Kuepper <jochen@uni-duesseldorf.de>
Organization: Heinrich-Heine-Universitaet
To: chemistry@www.ccl.net
Subject: AMD K6 BLAS
Date: Mon, 1 Mar 1999 10:23:14 +0100
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Dear All,

there are some Pentium optimized BLAS libraries for Linux/gcc on the net, but
does anybody know one that is optimized for an AMD-K6 (also Linux/gcc)
specifically ?

Greetings,
Jochen
-----------------------------------------------------------------------
  Jochen Küpper

  Heinrich-Heine-Universität Düsseldorf     jochen@uni-duesseldorf.de
  Institut für Physikalische Chemie I
  Universitätsstr. 1, Geb 26.43 Raum 02.29     phone ++49-211-8113681
  40225 Düsseldorf                             fax   ++49-211-8115195
  Germany             http://www-public.rz.uni-duesseldorf.de/~jochen
-----------------------------------------------------------------------


From chemistry-request@www.ccl.net  Mon Mar  1 04:35:50 1999
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	Mon, 1 Mar 1999 10:21:55 +0100
From: Jochen Kuepper <jochen@uni-duesseldorf.de>
Organization: Heinrich-Heine-Universitaet
To: "Gregory A. Landrum" <landrum@foreman.ac.rwth-aachen.de>,
        chemistry@www.ccl.net
Subject: benchmarking
Date: Mon, 1 Mar 1999 10:18:46 +0100
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On Don, 25 Feb 1999 Gregory A. Landrum wrote:
>Normally I stay silent on these things, but this comment was just a bit
>too indicative of general "benchmark abuse".

Absolutely.

>One more time, for good measure:
>If you want reliable benchmarks of *hardware* performance, you must
>compare the same programs on the different hardware.

Actually there are still many things to worry about then:
Compiler/Optimizer quality !
Math libraries !!!
 ...

You really need to test the system in the configuration you will run it,
otherwise there are just to many parameter to incorporate.

Greetings,
Jochen
-----------------------------------------------------------------------
  Jochen Küpper

  Heinrich-Heine-Universität Düsseldorf     jochen@uni-duesseldorf.de
  Institut für Physikalische Chemie I
  Universitätsstr. 1, Geb 26.43 Raum 02.29     phone ++49-211-8113681
  40225 Düsseldorf                             fax   ++49-211-8115195
  Germany             http://www-public.rz.uni-duesseldorf.de/~jochen
-----------------------------------------------------------------------


From chemistry-request@www.ccl.net  Mon Mar  1 09:16:36 1999
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Dear CCL readers,

I'm trying to freeze onde dihedral angle using PC-GAMESS but I'm having
problems. I tryed to use IFREEZ and IFZMAT but the program give me those
error messages:

1)For:   $ZMAT DLC=.T. IFZMAT(3)=12,11,9,8 FVALUE=60.000 $END
            
                       $

 LEGAL KEYWORDS FOR THIS GROUP ARE:
  IZMAT     SIJ       IJS       DLC     
 ERROR IN $ZMAT INPUT - ERROR


2)For: $STATPT NSTEP=500 opttol=0.0001  IFREEZ(3)=12,11,9,8  $END
          

 ****ERROR, YOU TRIED TO FREEZE INTERNAL COORDINATES WITHOUT DEFINING THE
INTERNALS
 OBTAINING INITIAL HESSIAN, HESS=GUESS   

My $data is in ZMT coordinates style generated by Molden.

Any hits will be appreciated !

Regards,
Demétrio Filho


_____________________________________

                Demetrio A. da Silva Filho
                   UNICAMP - IFGW
                    Prédio D - Sala 17
            CEP 13083-970 C.Postal 6165
                   Campinas - SP - Brasil
_____________________________________   


From chemistry-request@www.ccl.net  Mon Mar  1 15:14:41 1999
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From: "Diego S. Pedrosa" <diego@dqo.fcq.unc.edu.ar>
To: chemistry@www.ccl.net
Subject: HELP with HyperChem MD!!!! (fwd)
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Dear CCL'ers:

	I'm an undergraduate student at the Universidad Nacional de
Cordoba (Argentina), I'm almost at the end of my final work for the
graduation and I'm haveing some trubles with my calculations:
	I'm trying to do Molecular Dinamics of a sesquiterpene with Hyper
Chem (for Window$). My problem is that I need the "snapshots" of each step
of the MD in separate ".hin" files, and I can't do that (can't save each
structure in separate files), I'm kinda newbie with this MD calculations.
	I'll appreciate if anyone knows what can I do; I know Paolo
Mencarelli wrote a "script" to do that in his paper:

	The Conformational Behavior of n-Pentane: A Molecular Mechanics
and Molecular Dinamics Experiment, J. Chem. Ed., Vol 72, Num. 6, June
1995, pp 511.

but he don't gave the code of that script.

Thanks in advance...

			Diego.




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Date: Tue, 02 Mar 1999 00:07:26 +0300
From: "Victor E. Kuz'min" <victor@farlep.net>
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Subject: CCL:Drawings--->Stuctural file
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                                Dear Colleagues,
Whether there is a software for conversion of a graphics image of
molecular structure ( for example: *.gif, *.jpg, …. etc) in files such
as *.mol, *.hin, *.pdb, ….? This is a peculiar kind of OCR for the
structural formulas. It will enable for scanned drawings to get the
structural file. Is it possible? I shall be grateful for any guidelines
or tips.

With best regards,
                                          VEK

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Victor E. Kuz'min    |           National Academy of Science of Ukraine
 Head  Scientist       |         A.V.Bogatsky Phys.- Chem. Institute
Deputy Head of Department of Thermodynamics & Theoretical Chemistry
                      86 Lustdorfskaja doroga, 270080, Odessa, Ukraine
   Home:                                      Office:
38(0482) 631389                 38(0482) 225127   Fax 38(0482) 652012
victor@farlep.net                         vek@pci.farlep.net





