This is the electrostatic potential of a new, never before synthesized
'triple decker' organometallic 'sandwich compound', superimposed on its
electron density.  The synthesis and structure of the compound was just
recently published in Angew. Chem. Int. Ed. 2002, 41, No. 9.

I calculated the electron density and molecular electrostatic potential
using my normal set of Quantum Chemical software tools.  I generated the
electron density isosurface with my marching cubes code.  I used POV-Ray 3.5
for rendering with a mesh2 structure for the isosurface.   The superposition
of the electrostatic potential was done with a texture per vertex
specification in the mesh2 structure.  The textures were colors that
corresponded to the value of the electrostatic potential at each point on
the electron density surface.  Blue is negative (-0.2 units) and red is
positive (0.2 units).  The other colors ranged between blue and red in
value.  There are 256 colors used.

The spheres and rods viewable through the slightly transparent isosurface
are the atoms and bonds framework of the molecule.

Turned out rather nice.

Novel Triple Decker Organometallic Sandwich Compound - Potential on Density

Jim

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Attachments:
Download 'density_001.gif' (51 KB)

Preview of image 'density_001.gif'

A very nice image.  I would have thought, though, that the radicals
(methyls?) sticking out in fives would have been at random rotations rather than
aligned.  Hmm, on second thought, maybe that is the lowest energy state, and
what keeps the sandwich stable.  Just looking at the second layer there.
    This is a nice use of the software, and I imagine that somebody somewhere
working on MEMS and nanotech will be using POVray to start imaging some of their
work soon.

Cheers!

Chip Shults
My robotics, space and CGI web page - http://home.cfl.rr.com/aichip

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>Jim Kress <nos### [at] kressworkscom> wrote in message
news:3d3a5242@news.povray.org...
> This is the electrostatic potential of a new, never before synthesized
> 'triple decker' organometallic 'sandwich compound', superimposed on its
> electron density.  The synthesis and structure of the compound was just
> recently published in Angew. Chem. Int. Ed. 2002, 41, No. 9.
>
> I calculated the electron density and molecular electrostatic potential
> using my normal set of Quantum Chemical software tools.  I generated the
> electron density isosurface with my marching cubes code.  I used POV-Ray
3.5
> for rendering with a mesh2 structure for the isosurface.   The
superposition
> of the electrostatic potential was done with a texture per vertex
> specification in the mesh2 structure.  The textures were colors that
> corresponded to the value of the electrostatic potential at each point on
> the electron density surface.  Blue is negative (-0.2 units) and red is
> positive (0.2 units).  The other colors ranged between blue and red in
> value.  There are 256 colors used.
>
> The spheres and rods viewable through the slightly transparent isosurface
> are the atoms and bonds framework of the molecule.
>
> Turned out rather nice.
>
> Novel Triple Decker Organometallic Sandwich Compound - Potential on
Density
>
> Jim


Wow.. I feel stupid...

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"This is a nice use of the software, and I imagine that somebody somewhere
working on MEMS and nanotech will be using POVray to start imaging some of
their
work soon."

I already have.

Thanks.

Jim

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"Oldstench" <tha### [at] hotmailcom> wrote in message
news:3d3b8108@news.povray.org...
> >Jim Kress <nos### [at] kressworkscom> wrote in message
> news:3d3a5242@news.povray.org...
> > This is the electrostatic potential of a new, never before synthesized
> > 'triple decker' organometallic 'sandwich compound', superimposed on its
> > electron density.  The synthesis and structure of the compound was just
> > recently published in Angew. Chem. Int. Ed. 2002, 41, No. 9.
> >
[...]

> Wow.. I feel stupid...
>
Don't be...
Recently I read a thread between a couple of guys about network problems.
Maybe you can follow that without scratching your head, but I couldn't.
They were throwing with terms I never had heard of and I thought I knew
something about it. So, I have a lot to learn still.

Greetings,

Jaap Frank

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"Jim Kress" <nos### [at] kressworkscom> wrote in message
news:3d3a5242@news.povray.org...
> This is the electrostatic potential of a new, never before synthesized
> 'triple decker' organometallic 'sandwich compound', superimposed on its
> electron density.  The synthesis and structure of the compound was just
> recently published in Angew. Chem. Int. Ed. 2002, 41, No. 9.

I can't read the article (or can you reach it via internet?), so I ask you
directly. Is it one central atom (or ion) or are there two of them? And
what is it? Magnesium or a heavier kind?

> I calculated the electron density and molecular electrostatic potential
> using my normal set of Quantum Chemical software tools.

I am interested in this software. I have made pictures of the orbitals of
hydrogen for my students at school (see attachments) with formula's I
digged out of a very old quantum mechanic book that I stumbled over
in a second hand bookstore years ago. If it is possible to render
pictures of molecules with Molecular Orbitals with that software,
maybe I can persuade my school to buy it. Computer graphics make
students to take interest in subjects they otherwise ignore.

Further on you talk about electrostatic potential. Is it correct that you
mean with that the energy potential of a atom caused by the net charge
of the nucleus and his electrons?
If so, is it possible to calculate this for bounded atoms as well, using
Molecular Orbitals?

Regards,

Jaap Frank

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Attachments:
Download 'H_PROB_4F0_HIGH.PNG' (136 KB) Download 'H_PROB_3D0_HIGH.PNG' (138 KB)

Preview of image 'H_PROB_4F0_HIGH.PNG'

Preview of image 'H_PROB_3D0_HIGH.PNG'

??? Outlook Express thinks these .PNG files might contain a virus !!!!!!!
Has anybody else got the same experience ???
I can asure you that they are pictures and nothing else.

Jaap Frank.

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> I can't read the article (or can you reach it via internet?), so I ask you
> directly. Is it one central atom (or ion) or are there two of them? And
> what is it? Magnesium or a heavier kind?
>
There are 3 central atoms.  They are all Ruthenium (Ru).  The other 91 atoms
are Carbon, and Hydrogen.  The molecule is at the experimental geometry and
is a +2 ion with no unpaired electrons.

> I am interested in this software. I have made pictures of the orbitals of
> hydrogen for my students at school (see attachments) with formula's I
> digged out of a very old quantum mechanic book that I stumbled over
> in a second hand bookstore years ago. If it is possible to render
> pictures of molecules with Molecular Orbitals with that software,
> maybe I can persuade my school to buy it. Computer graphics make
> students to take interest in subjects they otherwise ignore.
>
See the Research Section of my website (http://www.kressworks.com/) for more
pictures of molecular orbitals.  It also has information about, and links
to, the software I used to generate the molecular orbitals, electron
density, molecualr electrostatic potential, and other properties.

> Further on you talk about electrostatic potential. Is it correct that you
> mean with that the energy potential of a atom caused by the net charge
> of the nucleus and his electrons?
> If so, is it possible to calculate this for bounded atoms as well, using
> Molecular Orbitals?
>
The electrostatic potential of the molecule represents the interaction
between the charge distribution of the molecule and a unit point charge
located at some position p.  It is calculated using molecular orbitals and
nuclear substructure that characterize the molecular system.

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Jaap Frank wrote:

> ??? Outlook Express thinks these .PNG files might contain a virus !!!!!!!
> Has anybody else got the same experience ???
> I can asure you that they are pictures and nothing else.

Kind of ironic; it's thanks to Microsoft that pictures can contain 
viruses anyway.  A picture with a virus!  How ridiculous is that?

-- 
___     ______________________________________________
  | \     |_         website: http://davidf.faricy.net/
  |_/avid |ontaine           email: <dav### [at] faricynet>

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On Wed, 24 Jul 2002 22:41:10 -0500, David Fontaine <dav### [at] faricynet>
wrote:

>Kind of ironic; it's thanks to Microsoft that pictures can contain 
>viruses anyway.  A picture with a virus!  How ridiculous is that?

Actually, a picture *can* contain a virus. I've seen a .jpg that can
be opened by ACDSee and PhotoShop, which is also an .exe which Windows
starts happily. NAV identified it as some Russian virus.


Peter Popov ICQ : 15002700
Personal e-mail : pet### [at] vipbg
TAG      e-mail : pet### [at] tagpovrayorg

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