Subject: Summary: visualisation of free radicals

From: Jeremy R Greenwood <[email-masked]>
Date: Tue, 18 Apr 1995 14:27:44 +1000 (EST)

Summary of responses to question concerning visualisation of localisation
of free-radicals.

Thanks to all who responded.

Original question:

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Secondly, I am interested in visualising localisation of free radicals
calculated by MOPAC or G92. Some kind of map of spin density would
seem to be an appropriate method. Can anyone suggest software (preferably
cheap or free!) which can extract and produce this kind of output?
I believe that Spartan has this capability, but is outside our price-range.

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From: Peter Fluekiger <[email-masked]>
To: [email-masked]
Subject: Molekel

Dear Jeremy,

thank you for your interest in Molekel. It is indeed esily possible to
visualize 3D (and 2D) representations of the spin density distribution with
Molekel, just based on the results of a Gaussian 92 computation (you need to
launch it with the keywords GFPRINT and POP=REG or POP=FULL). Unfortunately,
Mopac is not included yet - it wouldn't be that much work, but time is
lacking...

Here, I append a short description of Molekel:

Molekel is a tool for visualizing results of computational chemistry. Two
points have been stressed: first, it can be used as a routine tool for rapidly
generating views of electron or spin densities, orbitals, meps or vibrational
modes from the standard output files of the compoutational packages (or simply
molecular structures), and second, very nice and sophisticated views can be
generated for conferences or posters using recent techniques such as
1D-textures for representing surface properties and others.

What is still missing, even though it is planned for the future, is a molecule
editor. And well, it's a university development which means that we cannot
guarantee the reliability and support such as a commercial enterprise, and the
user's guide is still quite sparse.
Several research groups in Switzerland have been using Molekel for quite some
time to their entire satisfaction, and last year, we started commercializing
the package for 500.- swiss francs for non-profit organizations, and 5000.- for
commercial ones (i.e. ~US $ 380.- and 3800.-) for the licence for one group.
Molekel is running on practically all SGI workstations with hard- or software
zbuffer.

Unfortunately, we cannot provide test-licenses.

   I hope these indications are helpful for you!

        sincerely yours

                peter

Here is a cut-and-paste from a small leaflet describing Molekel:

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MOLEKEL is a powerful 3-dimensional molecular graphics package for the
interactive visual representation of molecular structures and properties. It is
mainly designed for generating detailed, easily interpretable and esthetically
appealing graphical output based on structural data and the results of
physico-chemical calculations. Due to the flexibility of the data- and
program-structure, various chemical systems ranging from small organic
compounds to large macro-molecules may be investigated, and due to its
modularity, additional interfaces and tools can easily be implemented.

MOLEKEL offers an intuitive and userfriendly graphical user-interface with
mouse-driven menus, file-browser, dialog-boxes and mouse-driven tools for
manipulating the represented 3D-objects.
Various models for data visualization can be chosen in MOLEKEL: wire-frame,
ball-and-stick, stick-only or spacefilling representation for the molecules;
dotted, chicken-wire, solid or semi-transparent representation for the surfaces
which may be cut by clipping planes. Object- and background colors can be
modified individually, and on machines which support texture-mapping, different
textures can be applied to all objects.
For maximum realism, shadows can be added to the scenes.

MOLEKEL contains various data-interfaces to external electronic structure
calculation program-packages:
        Gaussian, a library of ab initio quantum-chemistry methods
        Gamess,
        Hondo,
        Amoss, direct ab initio quantum-chemistry code
        deMon, density functional calculation code
        ADF, density functional calculation code
        Icon8, semi-empirical calculations based on the Extended Hueckel method
        EHProp, semi-empirical calculations of interaction energies based on
the
           Extended Hueckel method
        (Soon: Mopac, Mndo, Prddo).

For all of these packages, the standard output files can be read, the
structures can be extracted and the molecular orbitals, the spin density and
the electron density can be calculated and visualized. For ICON8 and EHProp
(and soon for Gaussian and Amoss) the input can be generated and the
calculations can be launched from within MOLEKEL.
Supplementary packages can easily be added to this list.
Connolly's MS-program is equally interfaced for generating molecular
dot-surfaces.

Internal modules of MOLEKEL allow the generation of solid models of different
properties: a fast (!) surface triangulation tool transforms dot-surfaces into
solid surfaces, and an iso-surface tool generates solid representations of
densities and wavefunctions. A contour tool allows the generation of
2D-contour-plots within the 3D-scene. Surface properties can either be
visualized using a color-code, or, on machines which support texture-mapping,
by quantized colors and contour-lines on the surfaces.

MOLEKEL allows the rapid investigation of results from external packages, as
well as the construction of complex graphical representations for publications
or conferences, and on demand, additional features for special applications may
be implemented additionally.

-- 
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Peter F. Fluekiger, Ph. D.
Scientific Visualization
Centro Svizzero di Calcolo Scientifico       Tel     :       (41) 91 50 83 27
Via Cantonale                                Fax     :       (41) 91 50 67 11
CH-6928 Manno (Switzerland)                  E-mail  : [email-masked]
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From: [email-masked]
Date: Wed, 5 Apr 1995 17:44:08 +0200
Message-Id: <[email-masked]>
To: [email-masked]
Subject: Free radicals

Dear Dr. Greenwood,

I think, you need the "free valence indices" for visualizing
free radicals. These were introduced in my paper I. Mayer,
Chem. Phys. Lett. 27, 290 (1983) with some correction in
Addendum to that paper: CPL 117, 396 (1985); also see
IJQC 26, 151 (1984) [addendum 28, 419 (1985)];  and papers
TCA 67, 315 (1985); IJQC 29, 73, 477 (1986) , etc.

You will get for each atom a number which is the measure of
the free spin on it - something as a "dot" on a chemical
formula of a radical.

If you are interested, I can send you routines which then you
can adapt to your programs.

Best regards,

Prof. Istvan Mayer
Central Research Institute for Chemistry
 of the Hungarian Academy of Sciences
E-mails: [email-masked]          and
         [email-masked] (or [email-masked]);
         [email-masked] (or [email-masked])