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PDB molecules Molecular Modelling

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The 2,3,7,8-tetrachlorodibenzo-p-dioxin molecule, is considered here as an example of a class of molecules which are composed of three six membered rings, specifically, oxanthrenes.

Dr. Thomas M. Zamis of Department of the Chemistry, University of Wisconsin - Stevens Point, WI, confirmed the technically correct Beilstein, CAS name. http://chemdept.uwsp.edu/tzamis/
Dr Zamis sent us a gif showing the numbering of dibenzo-p-dioxin, or oxanthrene.He also helped us to understand why the molecule is numbered the way it is, although his methodology was somewhat socratic. The molecule's popular name is 2,3,7,8-tetrachlorodibenzo-p-dioxin, or TCDD.
TCDD
Dr. Gerry Moss in personal communication informed us that the IUPAC actually prefers to name it as a substituted oxanthrene. The benzene rings can be considered as substituents fused to a central diheterabenzene ring.. ring shaded
orth meta para Looking at the molecule again, which something is para to which something else? Give up? Thought so.The terms, ortho, para and meta usually refer to substituents of a benzene ring as the diagram at left indicates.
But in the case of oxanthrene the [1,4] or "para," or simply, "p," refers to the positions of the oxygen atoms in the central 1,4 diheterabenzene ring viz. that ring itself. So that in effect there are two numbers assigned simultaneously to the oxygens of the molecule. That can be confusing. For the sake of simplification, the small case letter, "p" is used as in, dibenzo-p-dioxin. 1,4 diheterabenzeene shaded
When substituent groups are attached to the carbons of the benzene rings on either side of the central diheterabenzene ring, atoms are assigned numbers as shown in the diagram in order to arrive at a systematic name for the compound. Usually in the naming of compounds, it is the carbon atoms which are numbered. But in this case the oxygens are assigned numbers as well. We wish to thank Dr. Tom Zamis for his gif image showing the numbering of the parent oxanthrene component. numbering
Thus with an oxanthrene or dibenzo-p-dioxin substituted as shown, the compound is given the name 2,3,7,8-tetrachlorodibenzo-p-dioxin or 2,3,7,8-tetrachloro-oxanthrene. tcdd
With bromine similarly substituted, the name becomes, 2,3,7,8-tetrabromodibenzo-p-dioxin. tbdd

What is IUPAC?

INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY

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

IUPAC keeps the ducks in a row for chemists who use systematic names for compounds. Beilstein and CAS perform similar duck aligning functions. There must be gazillions of molecules so it's a big job and somebody has to do it, of course. We consulted the IUPAC for clear definitions.

Fused Ring and Bridged Fused Ring Nomenclature

http://www.chem.qmw.ac.uk/iupac/fusedring/FR22.html

"A heterotricyclic parent component that consists of two benzene rings fused to a 1,4- diheterabenzene in which the heteroatoms are the same is named from the appropriate replacement prefix (Table 1 of RB-1.1 in ref 9) and the suffix '-anthrene' with elision of the 'a'. For example:"

Thianthrene

"In an attached component prefix the ending '-ene' is changed to '-eno'. Appendix 2 includes this system for O, S, Se, Te, P, As, Si, B, and Hg (entries 63, 74, 79, 84, 89, 99, 109, 110, and 111 in appendix 2). The nitrogen analogue is an exception and is named phenazine. Boranthrene, oxanthrene, silanthrene and telluranthrene were not included previously (ref 3). Oxanthrene is still called dibenzo[1,4]dioxin by CAS and Beilstein."

"I am only concerned with the IUPAC recommended name. There are many other possible names of which Beistein ansd CAS usage is listed. It was because of the popular misuse of dioxin to mean the dibenzo[1,4]dioxin that we changed to oxanthrene." Gerry Moss

Oxanthrene is technically the name that IUPAC gives to our compound's parent component then except that Beilstein and CAS want to call it dibenzo[1,4]dioxin, or dibenzo-p-dioxin. Well they are the big dog and they wag the tail so it remains to be seen when the term oxanthrene will become more widely used or when the popular misuse of the term dioxin to mean the dibenzo[1,4] dioxin will fade away.

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