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PDB molecules Molecular Modelling

tcdd logo The 2,3,7,8-tetrachlorodibenzo-p-dioxin molecule, an oxanthrene, has three six membered rings.

TCDD has a heterotricyclic parent component that consists of two benzene rings fused to a 1,4- diheterabenzene in which the heteroatoms are the same, i.e., two oxygens. In these images just the nuclear centers are shown and the donut shaped hybridized molecular orbitals are not. Hybridization of the central diheterabenzene ring can be expected to restrict the degrees of freedom of the central portion of the molecule to a single plane. Fusion of the two benzene rings, which are themselves characteristically flat and planar, with the core diheterabenzene mid section, contribute even further to the overall planarity of the molecule. Consequently the statistcal probability that all of the atomic centers should lie in a single narrowly defined plane, is such that the molecule would be completely flat more than 99% of the time. Molecular modelling permits the molecule to be viewed from various perspectives. The result is that one can appreciate both its planar aspect and its unusually precise and perfect bilateral symmetries. 2,3,7,8-tetrachlorodibenzo-p-dioxin and dioxins in general are also interesting because there is a special convention for deriving it's systematic, or "IUPAC," name as well as disagreement as to the implimentation of that convention.

http://www.chem.qmw.ac.uk/iupac/
TCDD

Using Mac/PC Molecule, one may interactively manipulate the molcule in real time 3D using a variety of selective parameters, save views with scripted annotations, and export visual images at 8 or 24 bit depths.

One may also export movie files on both the Mac and PC. Using applications for changing movie files into gif animation files, one may prepare the animated files for web pages which can be viewed directly, obviating the need for plug-ins..

The people at Mac/PC Molecule can help users find relatively esoteric pdb files, for example the tcdd dioxin. Dioxins are a class of compounds sharing common characteristics. One can't just say dioxin and indicate one specific compound since a there are a variety of dioxins each having different chemical structures depending on which substituent groups they may contain. Upon recieving our second request in which we provided the accurate IUPAC name, Molecular Ventures, provided a .pdb file for tcdd which contained this annotation:

2,3,7,8-Tetrachlorodibenzo-p-dioxin occurs as a highly toxic impurity found in herbicides containing 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) and 2,4,5-T- derivatives, as well as in other chemicals synthesized using 2,4,5-trichlorophenol. The herbicide 2,4,5-T has been marketed in the United States since 1948. Production increased sharply between 1960 and 1970 when a 1:1 mixture of 2,4,5-T and 2,4-dichlorophenoxyacetic acid (2,4-D) was used as a defoliant in Southeast Asia under the names of "herbicide agent orange, herbicide orange, agent orange, and orange". During this 10-year period, about 106 million pounds of 2,4,5-T were sprayed.

Dr. Thomas M. Zamis at the Department of Chemistry, University of Wisconsin - Stevens Point, WI, in an apparent attempt to clarify things beyond any reasonable doubt, provided confirmation of the technically correct IUPAC name, a gif image of the conventional 2D structure,

TCDD,

and a gif depicting the numbering of the parent oxanthrene,

Oxanthrene numbering

He has a website with a large collection of molecule models. It is an especially convenient collection to browse because it is so well organized. Numerous trivial names for compounds are used which sometimes simplifies a search. It is geared toward the teaching aspects of chemistry with many general classes of molecules represented including for example even members of the simple paraffins. This is in sharp contradistinction to some of the other databases which are so large and all inclusive that the search methods must necessarily be so arcane as to render them useless (for Buddycom). He seems to be a Mac dude and that is reflected in the site's intuitive layout. It's easy to see why lots of people have links to the site.

Webpage: http://chemdept.uwsp.edu/tzamis/
Naming tcdd, click here.
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