From alexei@palladium.enscm.fr  Thu Jul 30 03:46:56 1998
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From: Arbouznikov Alexei <alexei@palladium.enscm.fr>
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To: CHEMISTRY@www.ccl.net
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Subject: numerical solution of Schroedinger equation 
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	Dear CCL'ers,

	I would be very much obliged to anybody who could give me
any references on the following subject:

	(1) numerical solution of Schroedinger equation for the simplest
two-electron systems (i.e., Helium atom or H2 molecule) - I believe, it's
impossible that such kind of work has never been done;

	(2) any available software for solving numerically the
partial differential equations with singularities. 

	Summary is guaranteed.

	Regards,

	Dr. Alexei Arbouznikov
        Ecole Nationale Superieure de Chimie,
	Laboratoire de Materiaux Catalytiques et Catalyse en
	Chimie Organique, UMR 5618 CNRS-ENSCM - Prof. F.Fajula,
        8, rue de l'Ecole Normale
        34296 Montpellier, Cedex 5
        FRANCE

        Telephone: (33) 4-67-14-72-68
        Fax:   (33) 4-67-14-43-49
        E-mail: alexei@palladium.enscm.fr 



From laaksone@csc.fi  Thu Jul 30 04:16:34 1998
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Date: Thu, 30 Jul 1998 11:12:04 +0300 (GFT Daylight Time)
From: Leif Laaksonen <laaksone@csc.fi>
To: Arbouznikov Alexei <alexei@palladium.enscm.fr>
cc: CHEMISTRY@www.ccl.net
Subject: Re: CCL:numerical solution of Schroedinger equation 
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Alexei,

Pekka Pyykkö, Dage Sundolm and I worked on the numerical solutions
for the Schrödinger and Dirac equations for diatomic molecules 
during the 80's. The numerical program for the Schrödinger equation
is avalailable at:

http://laaksonen.csc.fi/num2d.html

For some references to our work please have a look at:

http://laaksonen.csc.fi/publications.html

Regards,

-leif laaksonen

-------------------------------------------------------------------
Center for Scientific Computing    | Phone:      358 9 4572378
P.O. Box 405                       | Mobile:     358 400425203
FIN-02101 Espoo                    | Telefax:    358 9 4572302
FINLAND                            | Mail:  Leif.Laaksonen@csc.fi
-------- URL: http://laaksonen.csc.fi/leif.laaksonen.html ---------


On Thu, 30 Jul 1998, Arbouznikov Alexei wrote:

> 
> 	Dear CCL'ers,
> 
> 	I would be very much obliged to anybody who could give me
> any references on the following subject:
> 
> 	(1) numerical solution of Schroedinger equation for the simplest
> two-electron systems (i.e., Helium atom or H2 molecule) - I believe, it's
> impossible that such kind of work has never been done;
> 
> 	(2) any available software for solving numerically the
> partial differential equations with singularities. 
> 
> 	Summary is guaranteed.
> 
> 	Regards,
> 
> 	Dr. Alexei Arbouznikov
>         Ecole Nationale Superieure de Chimie,
> 	Laboratoire de Materiaux Catalytiques et Catalyse en
> 	Chimie Organique, UMR 5618 CNRS-ENSCM - Prof. F.Fajula,
>         8, rue de l'Ecole Normale
>         34296 Montpellier, Cedex 5
>         FRANCE
> 
>         Telephone: (33) 4-67-14-72-68
>         Fax:   (33) 4-67-14-43-49
>         E-mail: alexei@palladium.enscm.fr 
> 
> 
> 
> -------This is added Automatically by the Software--------
> -- Original Sender Envelope Address: alexei@palladium.enscm.fr
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>              Web: http://www.ccl.net/chemistry.html 
> 
> 


From elewars@alchemy.chem.utoronto.ca  Thu Jul 30 11:54:34 1998
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Date: Thu, 30 Jul 1998 11:54:30 -0400 (EDT)
From: "E. Lewars" <elewars@alchemy.chem.utoronto.ca>
Message-Id: <199807301554.LAA28780@alchemy.chem.utoronto.ca>
To: chemistry@www.ccl.net
Subject: TS BY GEOM OPT, KCAL AND HARTREES--RESPONSE


Thurs July 30

Yury Voloshin asked
1) How can a geom opt (rather than a TS opt) give a transition state?

2) How can one convert semiempirical energies, in kcal/mol, to hartrees, for
   comparison with ab initio values?

-----------

1)  If your input geom has the same symmetry as a TS (of about the about the
    same geom), a geom opt will take it to that TS. Examples:

          H
          |
          |           geom opt
   F ---- C ---- F      ----->   TS for (degenerate) Sn2 displacement
         -  \
        -     \
      H        H

         D3h

                                geom opt
    D3h ethane (eclipsed)  ----->    TS for interconversion of
                                     D3d (staggered) conformations


        N
    N       N
                  AM1 geom opt
    N       N     ---------------->   TS for degenerate interconv. of
        N                             3 N2

       D6h


     One can often find a TS this way. Of course a TS at one computational level
  may be a minimum or a higher-order saddle point at a fifferent level.
-----

 2)  As you imply, semiemp and ab initio E's refer to different things and so
     can't be directly compared. However, chemistry studies energy
     _differences_, not energies. To covert a semiemp deltaE to hartrees,
     divide by 627.5:

       H      H              H      CH3                    Z    -------
        \    /                \    /                             /|\
         C==C                  C==C                               |
        /    \                /    \      (AM1)                   |
      CH3     CH3           CH3     H                    deltaE   |
                                                                  |
        -2.28 kcal/mol         -3.35 kcal/mol               E  --------
            Z                        E

                                deltaE = (-2.28 - (-3.35))/627.5 hartrees

                                       =1.07/627.5  h = 0.00171 h


       Also: deltaE h/molecule x 2626 = deltaE kJ/mol
============

      E. Lewars
============================

From juanmi@blucher.qf.ub.es  Thu Jul 30 13:22:28 1998
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Subject: Re: CCL:gradients of overlap integrals
To: bittner@uh.edu (Eric R. Bittner)
Date: Thu, 30 Jul 1998 19:12:06 +0200 (DFT)
Cc: chemistry@www.ccl.net
In-Reply-To: <35BF464F.15FB@uh.edu> from "Eric R. Bittner" at Jul 29, 98 10:57:03 am
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> We need to calculate the gradient of an overlap integral
> between tight-binding basis functions. 
> i.e. we need
> d/dx <psi_a | psi_b>  

You may take a look at 
F.X.Gadea, M.Pelissier, J. Chem. Phys 96 (1990) 545
They use finite increments, i.e.
d/dx<psi_a | psi_b> \approx (1/dx)(<psi_a | psi_b(x+dx)> - <psi_a | psi_b(x) >)
in order to compute radial coupling terms between functions.
Recently I've been working on partially analytical computation of these terms;
computing d(psi_b)/dx is quite straightforward when psi_b is a gaussian 
function. 

Hope it helps, 
JM
-- 
LIFE IS SO UNCERTAIN - EAT DESSERT FIRST 
                                 
Juan Miguel Bocanegra Moron (mailto:juanmi@blucher.qf.ub.es)
Grup de Cinetica i Dinamica de Reaccions Elementals     
DEPARTAMENT DE QUIMICA FISICA-UNIVERSITAT DE BARCELONA    
Marti i Franques, 1  08023 Barcelona   SPAIN                	 
tel: ++34 93 402-1224    

From fabio_valentino@hotmail.com  Wed Jul 29 04:43:49 1998
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 Dear All,

 In order to simulate a protein with water (SPC/E) in
a cubic box, one should use boundary conditions 
(usually periodic) and minimum image convention.
Should one apply "minimum image convention"
to protein atoms or only for the water molecules ?
Could you please provide me with more details and
didatic references ? Thanks in advance.

Fabio Valentino, M.Sc. student
fabio_valentino@HOTMAIL.COM




From ymumjc@nessie.mcc.ac.uk  Wed Jul 29 10:29:27 1998
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From: Jonathan Connor <Jonathan.Connor@nessie.mcc.ac.uk>
Message-Id: <199807291428.PAA03644@nessie.mcc.ac.uk>
Subject: postdoctoral vacancy
To: chemistry@www.ccl.net
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POSTDOCTORAL RESEARCH ASSOCIATE


New Theories of Chemical Reactions and Molecular Collisions


Applications are invited for a postdoctoral research associate position 
funded by the UK Engineering and Physical Sciences Research Council.

The research involves the development of novel theories for 
understanding the dynamics of chemical reactions and molecular 
collisions.  There are two complementary themes to the research: 

	(a) the dynamics of light atom transfer reactions, which involves
 computationally intensive scattering calculations.
 	(b) new semiclassical theories for understanding the angular 
scattering of reactive and inelastic collisions.

Examples of our recent research include: J. Chem. Phys. 1998 (108) 5695; 
ibid. 1996 (104) 2297; J. Chem. Soc. Faraday Trans. 1997 (93) 709; J. Comput. 
Appl. Math. 1997 (82) 447; Chem. Phys. 1996 (207) 461. Excellent
computational facilities are available for the research including
supercomputers and workstations.

The research on the dynamics of light atom transfer reactions involves 
collaboration with Professor G C Schatz, Dept. of Chemistry, Northwestern 
University, Evanston, Illinois, USA, and some travel to the USA is possible. 

The appointment is for 2 years. Salary in the range  15159-22785 UK 
pounds plus membership of the Universities Superannuation Scheme.

Candidates with strengths in either of the above themes (or both) should 
send their curriculum vitae and names of two referees to:

Professor J.N.L. Connor		Tel:  (+44)-161-275-4693/4686
Department of Chemistry		Fax:  (+44)-161-275-4734
University of Manchester
Manchester M13 9PL 
England	

Email: J.N.L.Connor@Manchester.ac.uk

-- 
******************************************************************************
 Professor J.N.L. Connor,     Phone(direct line): 0161-275-4693 (national)
 Department of Chemistry,                     :+44-161-275-4693 (international)
 University of Manchester,
 Manchester M13 9PL,            Phone(secretary): 0161-275-4686 or 4600
 England.                                    Fax: 0161-275-4734 or 4598  
****************************************************************************** 



From castejon@kbw350.chem.yale.edu  Wed Jul 29 13:25:23 1998
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Date: Wed, 29 Jul 1998 13:24:24 -0400
From: castejon@kbw350.chem.yale.edu (Henry J. Castejon)
Message-Id: <9807291724.AA14932@kbw350.chem.yale.edu>
To: CHEMISTRY@www.ccl.net





Hello everyone:

	Can someone help me with the following:

	I want to do molecular orbital calculations on second and third
	row transition metals. The compounds contain many more than one
	metal atom. (four or five). Consequently, I'm looking for some
	software capable of doing that. Gaussian doesn't have basis
	set for such metals and it may be a software using plane wave
	or something else.

	I will appreciate if someone can give a hint on this.
	Ah! I forgot a minor detail if the software is free better.
	Although I may be willing to spend some money on it.

	Thanks a lot for anything you can do. If I get a good compilation
	of answers I will summarize for everybody.

	Henry.




From desingh@mailbox.syr.edu  Wed Jul 29 14:28:35 1998
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Date: Wed, 29 Jul 1998 14:28:34 -0400 (EDT)
From: Deepak  Singh <desingh@mailbox.syr.edu>
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Hi netters,

	Is anyone aware of computational/theoretical work on the effects
of dephasing on virtual state lifetimes in multi-photon spectroscopy?  I
will summarize any answers that I receive.


Regards

Deepak.



From dons@hamilton.math.missouri.edu  Thu Jul 30 16:51:44 1998
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From: "Don Steiger" <dons@hamilton.math.missouri.edu>
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Date: Thu, 30 Jul 1998 15:51:42 -0500
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I am a math graduate student and working with one of the theoretical chemist at
the university here I developed a multipole algorithm for calculating coulomb
interactions.  With some modifications, this method can be used as a rapid
screening procedure for the electrostatic version of the docking problem.
The chemist that I am working with feels that this is a very important problem
in the area of drug design and that I should pursue it further.  In helping me
to decide if I should pursue this, I was wondering if someone could briefly
summarize the state of the art in this field.

I thank you in advance.

-- 
Don Steiger
dons@hamilton.math.missouri.edu

From dino@eik.bme.hu  Thu Jul 30 19:03:31 1998
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Date: Fri, 31 Jul 1998 01:03:29 +0200 (MET DST)
From: SZIEBERTH Denes <dino@eik.bme.hu>
To: chemistry@www.ccl.net
Subject: hyperfine constants summary
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the original message was:



----------------------------------------------------------------------
 Date: Mon, 20 Jul 1998 08:58:48 +0200 (MET DST)
From: SZIEBERTH Denes <dino@goliat.eik.bme.hu>
To: chemistry@www.ccl.net


 Dear CCL -ers

Calculated ESR hyperfine constants are sometimes reported in the
literature in MHz, and sometimes in Gauss. Could someone tell me which is
the more accepteble and how to convert between the two values?

            Denes Szieberth
            dino@goliat.eik.bme.hu



-------------------------------------------------------------------------


thanks for all the responses




*********************************************************************
From: David Close <closed@Access.ETSU.Edu>
Subject: hyperfine couplings


  Dear Denes:
  Hyperfine couplings are measured in magnetic field units
of Gauss.  Actually, the proper MKS unit is now the mT where
1 mT = 10,000 Gauss.
  If one wants to convert Gauss to frequency units (MHz) the
conversion is A(MHz) = 2.80247 a(Gauss).  Strickly speaking, this
factor is based on the g value of the free electron.
  Regards, Dave Close
-------------------------------------------------------
David Close                     Dept of Physics
closed@access.etsu-tn.edu       East Tennessee State
1 (423) 439-5646                Johnson City, TN, USA



Date: Mon, 20 Jul 1998 18:31:49 -0500 (CDT)
From: Sukumar <sukumar@tw515a.chem.mu.edu>
To: dino@eik.bme.hu
Subject: Re: ESR hyperfine constants

 
Sorry, I think I must have given you the values for the proton, while you
want 
for ESR (as you know, Gauss and Tesla are units of magnetic field strength
or 
magnetic flux density, while Hz and MHz are units of frequency). Anyway:
for proton resonance, 1 mT = 23.48660  MHz or 1 MHz = 0.04257747 mT
(milliTesla)
for electron resonance, 1 mT = 0.0356825 MHz or 1 MHz = 28.02494 mT
(milliTesla)
The conversion 10000 Gauss = 1 T (tesla) is, of course, the same by
definition.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/  Dr. N. SUKUMAR             /  Tel (O): (414)288-6753  /
/  Department of Chemistry    /      (R): (414)244-2786  /
/  Marquette University       /  Fax  :   (414)288-7066  /
/  P.O.Box 1881               ~~~~~~~~~~~~~~~~~~~~~~~~~~~/
/  Milwaukee, WI 53201-1881                              /
/  Email : sukumar@tw515a.chem.mu.edu                    /
/  http://www.thch.uni-bonn.de/tc/sukumar.html           /
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Date: Tue, 21 Jul 1998 09:24:21 +0200 (MES)
From: Bernd Engels <bernd@rs5.thch.uni-bonn.de>
To: SZIEBERTH Denes <dino@eik.bme.hu>
Subject: Re: CCL:hyperfine coupling

> 
> 
> 
>  Dear CCL -ers
> 
> Calculated ESR hyperfine constants are sometimes reported in the
> literature in MHz, and sometimes in Gauss. Could someone tell me which
is
> the more accepteble and how to convert between the two values?
> 
>             Denes Szieberth
>             dino@goliat.eik.bme.hu
> 
dear denes

it depends. if you look in high resolution spectroscopy they
mostly uses MHz. If you have ESR people, they use gauss, because
they have a magnetic field which with they make the measurements.
The conversion factor is 2.85025 MHz/Gauss

Needles to say, that Gauss is not an 'appropriate unit',
because it is related to the magnetic field, while the hyperfine
coupling constants are independent of the magnetic field!

But you cares

Bernd Engels

Date: Mon, 20 Jul 1998 15:12:26 +0200 (MET DST)
From: Andrzej Szyczewski <aszy@amu.edu.pl>
To: dino@goliat.eik.bme.hu
Subject: MHz

Dear Colleagues,
1G=2.8MHz. I would be very appeciate to obtain the information which
program do you use to calculate the ESR hyperfine splittings.
With best regards.
Yours sincerely
Andrzej

==============================================================
Dr. Andrzej Szyczewski      |                                |
Institute of Physics,       |   e-mail: aszy@amu.edu.pl      |
A.Mickiewicz University     |                                | 
Umultowska 85,              |                                |   
61-614 Poznan/Poland        |       fax: (4861) 821-79-91    | 
============================================================== 






From kotelyan@plmsc.psu.edu  Thu Jul 30 20:52:33 1998
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Date: Thu, 30 Jul 1998 20:52:55 -0400 (EDT)
From: Mike Kotelyanskii <kotelyan@planck.plmsc.psu.edu>
To: Don Steiger <dons@hamilton.math.missouri.edu>
cc: chemistry@www.ccl.net
Subject: Re: CCL:Drug design
In-Reply-To: <9807301551.ZM23337@hamilton.math.missouri.edu>
Message-ID: <Pine.SUN.3.91.980730204910.21296C-100000@planck>
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Check out papers by 
Greengard and Rokhlin,
S.Lustig and N.J.Wagner et.al.
sorry don't have them handy, 
these are all quite recent publications, last maybe 4-5 years,
I am sure you'll find it in the database,

Hope this helps,
Mike

-------------------------------------------------------------------------------
Michael J. Kotelyanskii	                     Phone (814) 863 43 81
Polymer Science Program			     FAX   (814) 865 29 17
Department of Materials Science and
Engineering                                  kotelyan@plmsc.psu.edu
Pennsylvania State University                http://www.plmsc.psu.edu/~kotelyan
University Park, PA 16802, USA
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On Thu, 30 Jul 1998, Don Steiger wrote:

> I am a math graduate student and working with one of the theoretical chemist at
> the university here I developed a multipole algorithm for calculating coulomb
> interactions.  With some modifications, this method can be used as a rapid
> screening procedure for the electrostatic version of the docking problem.
> The chemist that I am working with feels that this is a very important problem
> in the area of drug design and that I should pursue it further.  In helping me
> to decide if I should pursue this, I was wondering if someone could briefly
> summarize the state of the art in this field.
> 
> I thank you in advance.
> 
> -- 
> Don Steiger
> dons@hamilton.math.missouri.edu
> 
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