From ADRIAN@WCHUWR.CHEM.UNI.WROC.PL  Wed May 20 07:07:43 1998
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From: "Adrian Radomir Jaszewski" <ADRIAN@WCHUWR.CHEM.UNI.WROC.PL>
Organization:  University of Wroclaw (Chemistry)
To: chemistry@www.ccl.net
Date:          Wed, 20 May 1998 13:07:12 GMT+2
Subject:       ESR(EPR) spectra; G-tensor calculations
Priority: normal
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Dear CClers,


I'm interested in application of DFT calculations in determination of the 
geometry and magnetic parameters (isotropic and anisotropic) of  organic radicals.
I know that Gaussian94 produces output called "Fermi Contact Analysis" for
each atom in the molecule.These values can be easily convert to isotropic
EPR (ESR) hyperfine coupling constants. 
In order to perform G-TENSOR calculations I used the following options in the
input:
# PROP=EFG IOp(6/17=2,6/26=4). 
There are several sections in the output:
 
**********************************************************************
            Electrostatic Properties Using The SCF Density
 **********************************************************************

              Electrostatic Properties (Atomic Units)

 -----------------------------------------------------------------
    Center     Electric         -------- Electric Field --------
               Potential          X             Y             Z
 -----------------------------------------------------------------
 -----------------------------------------------------
    Center         ---- Electric Field Gradient ----
                     XX            YY            ZZ
 -----------------------------------------------------
 -----------------------------------------------------
    Center         ---- Electric Field Gradient ----
                     XY            XZ            YZ
 -----------------------------------------------------
 -----------------------------------------------------
    Center         ---- Electric Field Gradient ----
                   ----       Eigenvalues       ----
 -----------------------------------------------------
 -----------------------------------------------------
    Center         ---- Electric Field Gradient ----
                       ( tensor representation )
                   3XX-RR        3YY-RR        3ZZ-RR
 -----------------------------------------------------
 -----------------------------------------------------
    Center         ---- Electric Field Gradient ----
                       ( tensor representation )
                   ----       Eigenvalues       ----
 -----------------------------------------------------
 
but I don't know how to comprare these calculated values with 
the anisotropic parameters derived from the experiment - EPR
(ESR) spectrum of the radical.

Could anyone direct me to the proper references and/or shed some
light into this topic?

Many Thanks

Adrian R. Jaszewski


 --------------------------------------------------------------
 \                       Adrian R. Jaszewski                   /
 \              Department of Chemistry                        /
 \                  University of Wroceaw                      /
 \       14 Joliot-Curie St., 50-383 Wroceaw, Poland           /
 \       e-mail: adrian@wchuwr.chem.uni.wroc.pl                /
 --------------------------------------------------------------

From fdeprof@ulb.ac.be  Wed May 20 10:23:22 1998
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Dear,

Can anybody provide me with reference concerning the calculation of the
integral: 

I=integral(rho(r)rho(r')drdr'/|r-r'|) where rho(r) and rho(r') are
expressed as a sum over Slater type orbitals. 

best regards,

F. De Proft 
Free University of Brussels



From armel@fluo.univ-lemans.fr  Tue May 19 04:09:52 1998
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Date: Tue, 19 May 1998 10:12:47 +0200
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From: Armel Le Bail <armel@fluo.univ-lemans.fr>
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STRUCTURE DETERMINATION BY POWDER DIFFRACTOMETRY
                                         ROUND   ROBIN
       Organisers: Armel Le Bail (University of Le Mans) and
                          Lachlan Cranswick (Daresbury Laboratory).

      (Deadline for submission of solutions - June 30, 1998)

           http://fluo.univ-lemans.fr:8001/SDPDRR/

This is to announce the availability of powder diffraction data
as part of the Structure Determination by Powder Diffractometry
Round Robin (SDPDRR).

Participants have the option of solving one or both of two samples:
   i)  An Inorganic Phase
   ii) An Organic Pharmaceutical Compound

The data and information on the samples can be emailed, if web
links are too slow or congested.  A poster for pinning on department
bulletin boards is available on the web-site.

Background and protocol are available from the website.

A summary of results will be presented at an invited talk on
"Trends in Structure Determination from Powder Diffraction"
at the August 1998 ECM-18 meeting in Prague.

Armel Le Bail     (E-mail: armel@fluo.univ-lemans.fr)
Lachlan Cranswick (E-mail: l.cranswick@dl.ac.uk)



From patrikj@moore.Kemi.UU.SE  Tue May 19 04:11:11 1998
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From: "Patrik Johansson" <patrikj@moore.Kemi.UU.SE>
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Date: Tue, 19 May 1998 10:07:37 +0000
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Dear CClers

I would like to thank for the response I got from my posting regarding IR/Raman
spectra from calculated values. I have not had time to look them up to see what
suits me best, aslthough I suspect that I was not clear that I would need a
possibility to manually edit the width of each peak to make a kind a best fit
with several experimental spectra, anyway, here is a summary of the replies
until now. I hope that it will help someone else too.

I'm especially grateful to Jens from Roskilde who sent a
simple basic program (LORENTZ) which I include in the summary ( the mail from
him is in Danish, readable for me being Swedish, but probably hard for most of
you to grasp ;-)


best regards, Patrik

//My original query :

Dear CCLers

Does anyone know of a program which can be used to construct an artificial
vibrational spectrum from a Freq calculation in G94 or similar e.g. using the
 .log file or .chk file ?

For my purpose it would be nice if overlapping bands, overtones and mixed
bandforms could be treated as well as the possibility to change the FWHH
parameter for each band individually.

Thanks for any answers and of course I will summarise the replies.

Patrik


//Dear Patrik,

I think that you may use the Gauss View to your purpouses. With this
program you can visualize all the resouts using the .log or .chk files.
I hope that this clue could be useful.

Sergio Augusto Jardino Filho
sjardino@quim.iq.usp.br
Intituto de Quimica - Universidade de Sao Paulo
Brazil
hi...

//You could try inporting the freq file into a prog like hyperchem...
which would draw a vib spectrum...
Megan Govender <Megan.Govender@eskom.co.za>

//Kaere Patrik,

nedenstaaende finder du listning af et lille BASIC-program "Lorentz"
der producerer et 'kunstigt spektrum' under antagelse af Lorentz
linieform.  Programmet laeser input fra en fil, der indeholder det
beregnede spektrum Xi, Yi, hvor Xi er boelgetallet (eller
tilsvarende) og Yi er intensiteten (eller tilsvarende):

512.62  7.43
517.73  1.19
719.45  170.34
 .
 .
0 0

Inputfilen skal slutte med '0 0' som vist.  Output skrives paa samme
maade i en fil, i form af punkter paa en spektralkurve bestaaende af
bidrag fra (overlappende) Lorentz-linier.  Denne fil kan laeses ind i
et grafik-program til display, editing, og udskrift af det kunstige
spektrum.  Jeg bruger ORIGIN til dette formaal.

> For my purpose it would be nice if overlapping bands, overtones and mixed
> bandforms could be treated as well as the possibility to change the FWHH
> parameter for each band individually.

Det lille program "Lorentz" er meget simpelt og antager samme HWHM
(Half-Width at Half-Maximum) for alle linier; HWHM = 1 - 3 cm-1 synes
passende for de fleste IR spektre (vaerdien inputtes fra keyboard).
Indenfor den harmoniske tilnaermelse har overtone- og
kombinationsbaand zero-intensitet og vil normalt ikke blive beregnet.

Mange hilsener, Jens >--<



10 '***************************************************************
20 '
30 '                      * LORENTZ *
40 '
50 '              Jens Spanget-Larsen, Oct. 1997
60 '
70 '***************************************************************
80 DEFINT I,J,K,L,M,N : DEFDBL A-H,O-Z
90 OPTION BASE 1
100 DIM X(200),S(200)
110 PRINT : PRINT "Program LORENTZ" : PRINT
120 LINE INPUT "Input File? ", E$
130 LINE INPUT "Output File? ", F$
140 OPEN "I",#1,E$
150 OPEN "O",#2,F$
160 PRINT "Lorentzian Lineshape:"
170 INPUT "   Half-Width at Half-Maximum (HWHM)";HWHM
180 ' PRINT#2, "Lorentzian Lineshape, HWHM ="; HWHM
190 PRINT "Output-Frequency Range:"
200 INPUT "   Minimum";XMIN
210 INPUT "   Maximum";XMAX
220 PRINT "Read Input File:"
230 N=0
240 N=N+1
250   INPUT#1, X,S
260   IF X=0 THEN 300
270   X(N)=X : S(N)=S
280   PRINT X(N);S(N)
290   GOTO 240
300 N=N-1
310 DX=HWHM/5! ' steplength determined as a fraction of HWHM
320 PRINT : PRINT "Computing";1+INT((XMAX-XMIN)/DX);"Output Points...."
330 DMAX=HWHM*100! ' this is for speed; can be changed or omitted
340 B=HWHM^2
350 XL=XMIN-DX
360 XL=XL+DX
370   IF XL>XMAX THEN 460
380   SL=0
390   FOR I=1 TO N
400     D=ABS(XL-X(I))
410     IF D>DMAX THEN 430
420     SL=SL+S(I)*B/(B + D^2)
430   NEXT I
440   PRINT#2, USING "######.####";XL,SL
450 GOTO 360
460 PRINT : PRINT "End of RUN"
470 PRINT : PRINT "To Quit: Enter 'SYSTEM'"
480 END






=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
JENS SPANGET-LARSEN         Phone:  +45 4674 2000  (RUC)
Department of Chemistry             +45 4674 2710  (direct)
Roskilde University (RUC)   Fax:    +45 4674 3011
P.O.Box 260                 E-Mail: JSL@virgil.ruc.dk
DK-4000 Roskilde, Denmark   http://www.rub.ruc.dk/dis/chem/psos/
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

//I'm not quite sure but AniMol should do it. From other side it shuldn't be to
complicated to make it with any spreedshet with graphic (to complicated means
not time consuming).Krzys Radacki

//--hello patrick,

try MOLDEN. This is avery good visualizer for Gaussian output.

look at

http://www.caos.kun.nl/

go in the directory modeling. Klick on Molden (one program among others in
this directory)

hope this helps,

christoph
----


Christoph Widauer
Laboratorium f. Anorganische Chemie
ETH-Zentrum CAB B24.1-3
Universitätsstrasse 6
CH-8092 Zuerich


         end of summary


--
Dr Patrik Johansson
Inorg. Chem. Angstromlaboratory
Box 538 SE-751 21 Uppsala
Uppsala University SWEDEN
patrikj@moore.kemi.uu.se

-- 
Dr Patrik Johansson
Inorg. Chem. Angstromlaboratory
Box 538 SE-751 21 Uppsala
Uppsala University SWEDEN
patrikj@moore.kemi.uu.se


From s.m.todd@chem.hull.ac.uk  Tue May 19 06:12:14 1998
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Cheers for the replies regarding my question on dipole moments. The
replies are all summarised below.

My original post :

Hi all...

I have recently been doing some dipole moment calculations using the AM1

and PM3 semi-empirical methods in Hyperchem. I have been trying the
caculations at different torsion angles and obtaining some reasonable
results. However, occasionally a difference as small as 10 degrees makes

the dipole moment value increase from 4D to about 4000D. Has anyone else

had this problem ? What do people think of the accuracy of
semi-empirical calculations for such properties as dipole moments ?

Also, when the calculations were repeated under Mopac/AM1 and Mopac/PM3
in Cerius2 they yielded reasonable results. I presume this is to do with

the individual ways in which the two similar methods are implemented
under different packages (ie Hyperchem and Mopac). Has anyone any ideas
on this or any references to work done on this ?



==================

I'm not an expert in computational chemistry, but you might want to look

at
an article by Storer et. al. J. Comp.Aided Mol. Design 9 (1995) 87-110
where
roughly 200 AM1 and PM3 dipole moments for different neutral molecules
are
compared with those obtained from an alternative charge mapping method.
The
RMS errors reported in this article are 0.30 D and 0.26D respectively
for
the AM1 and PM3 semi-empirical methods. The point of the article is to
offer
an alternative charge model with improved accuracy.  Hope this helps
answer
your question.

Brian Williams, Chemistry, Bucknell University


======================
>From : Dr. Jose Luis Garcia de Paz

Hi

Mulliken charges an dipole moments when heteroatoms are
included are often unreliable at PM3 level due the parametrization.
They are much better at AM1 level . However PM3 geometries are
usually better than the AM1 ones. Regards

Jose

==================

This seems to be a bug in Hyperchem. Semiempirical dipole moments may
be not perfect, but they are not *that* bad. In fact, 4000D molecular
dipole moment would be very strange coming from any method: it implies
that your molecule has two electron-sized local charges separated by
almost 1000 angstrom. Or two 10e charges at 100 angstrom, etc.

Regards,

/Serge.P
===================
--

"I used to think the brain was the most important organ in the body,
'til I realized yeah, look what's telling me that."
                               -- Emo Phillips

        mail to : S.M.Todd@chem.hull.ac.uk
        web-site: http://www.hull.ac.uk/php/chpsmt/




--

"I used to think the brain was the most important organ in the body,
'til I realized yeah, look what's telling me that."
                               -- Emo Phillips

        mail to : S.M.Todd@chem.hull.ac.uk
        web-site: http://www.hull.ac.uk/php/chpsmt/




From tcundari@msuvx2.memphis.edu  Tue May 19 10:49:54 1998
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Date: Tue, 19 May 1998 09:48:43 -0500
From: "Thomas R. Cundari" <tcundari@msuvx2.memphis.edu>
Subject: Re: CCL:G:convergence criterion in SCF for calculation of
 polarizability
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Dear Patrick,

You must be very careful in calculating polarizability and related nonlinear
optical properties as these require very careful attention to the SCF 
convergence criteria than normal electronic structure calculations. My 
colleague here @ U of of Memphis, Henry Kurtz, has a chapter in an upcoming
issue of Reviews in Computational Chemistry that touches upon this.

In a recent paper in collaboration with Henry (Cundari, Kurtz & Zhou
J Phys Chem, A, 1998, 102, 2962) that investigates the NLO props of 
inorganic complexes we used a convergence of 10^-10 plus several other
options relating to the size of integrals that could be ignored.

Tom Cundari


At 09:26 PM 5/19/98 +0800, you wrote:
>Hello!  In Gaussian 94, the SCF convergence will be finished when a 
>specific density-based convergence criterion (10^-N) is met.  What is the 
>convergence criterion suitable for calculation of polarizability?  Of 
>course, 10^-8 is the best.  However, it will be paid much computational 
>time.  Is it suitable for choosing 10^-4?
>
>Thank you for your attention.
>
>Patrick Pang  
>
==========================================================================
Professor Tom Cundari		phone:901-678-2629 
Department of Chemistry		email: tcundari@memphis.edu
University of Memphis		FAX: 901-678-3447
Memphis, TN 38152-6060		www.chem.memphis.edu/compchem.html

Research: Comp inorganic chemistry, artificial intelligence apps in
	  chemistry; catalysis; advanced materials; ab initio, semi-
	  empirical & MM modeling of metal complexes

      *** Starting Fall '98 @ UofM: PhD w/ concentration in Comp Chem ***
==========================================================================


From dew01@xray5.chem.louisville.edu  Tue May 19 14:39:52 1998
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From: "Donald E. Williams" <dew01@xray5.chem.louisville.edu>
Message-Id: <9805191443.ZM12041@xray5.chem.louisville.edu>
Date: Tue, 19 May 1998 14:43:06 -0400
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	There seems to be a widespread misunderstanding that an ordinary
hydrogen bond (say O-H...O) can be modeled with a purely electrostatic
potential by "dumping everything into electrostatic parameters".  If anyone
knows of such a model, I would like to hear about it.
	There is a parameterization called the "disappearing hydrogen" model of
the OHB.  In this model, electrostatics are included, but also (and very
importantly) the repulsion of the hydrogen atom is set to zero, quite a drastic
change from a normal hydrogen atom.  It is easily shown that the effect of
eliminating hydrogen repulsion is by far more important than the
electrostatics.

>decompose an HB into its "electrostatic" and "covalent" contributions. An
>"ordinary" HB (OHB) has both electrostatic and covalent components, although
>it can be reasonably modelled by classical force fields by dumping everything
>into electrostatic parameters. An OHB can be neutral or charged. A charged

-Donald Williams

-- 
Dr. Donald E. Williams		email:dew01@xray5.chem.louisville.edu
Department of Chemistry
University of Louisville	phone:502-852-5975
Louisville, KY 40292		fax:  502-852-8149


From dqua@san.rr.com  Wed May 20 19:52:08 1998
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Subject: RE: Question about CERIUS 2
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Hi David...  which module of C.2 is that?  I know we support volume
descriptors in such places as QSAR, but I can't seem to recall anything
about "free volume." I also asked a couple of my colleagues regarding this,
and I got the same reply. How did you discover this calculation?

Sincerely,
Derick J.R. Qua
Sr. Software Engineer/Physicist
Molecular Simulations Inc. (http://www.msi.com)
9685 Scranton Road
San Diego, CA US


> -----Original Message-----
> From: Computational Chemistry List
> [mailto:chemistry-request@www.ccl.net]On Behalf Of
> David De Vito
> Sent: Monday, May 18, 1998 23:45
> To: CCL
> Subject: CCL:Question about CERIUS 2
>
>
> We have purchased the Cerius 2 programm package and I have
> a little question about it.
>
> I tried to use the 'free volume' calculation option and I'd like
> to know how the programm make this evaluation since I don't find any
> information about it in the help and manuals.
>
> The help support said me since we don't have any
> "maintenance" we can't
> obtain any answer in case of problems... That's a pity, really !
>
> Thanks in advance for the very helpfully explanations and
> best regards.
>
>
> Nice day for all the CCL people, D. De Vito.
>
>
> ****************************************************************
>
> D. De Vito
> Department of Physical Chemistry
> Group of Prof. Weber (Computational Chemistry)
> University of Geneva
> Office 106 - Sciences II
> 30, Quai Ernest-Ansermet
> 1211 Geneva 4 / Switzerland
> +4122 / 702.65.35 (Office)
> +4179 / 310.05.76 (Mobile)
> +4122 / 733.38.35 (Home)
> http://lcta.unige.ch/~devito (Personal Page)
> http://www.unige.ch/sciences/chimie (Web Master)
>
> ****************************************************************
>
>
>
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> -- Original Sender Envelope Address: David.DeVito@chiphy.unige.ch
> -- Original Sender From: Address: David.DeVito@chiphy.unige.ch
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