[markartist]

Hi,

Symbolic interactionists (sociological theory) claim that people are social actors with many roles that change with context.  In this context I am a well schooled visual artist interested in the visual representation (models) of molecules.  In particular, I am interested in the most basic rules that found representational molecular modeling.

For example, a given molecule consists of five atoms.  One of one kind of atom and four of another kind.  The four are shown connected the one.  Three of the bonds are represented by a straight line, the fourth by a chevron looking symbol.  The question then is why?  What rule is in play to say show these bonds using this symbol and this bond using that symbol.  Is there a lexicon or dictionary of the rules of molecular modeling?

While I have looked at a fair amount of information and I understand some of the representational why, I cannot figure out or find statements explaining why other things are done within the particular theory or strand of modeling.  There are computer based applications that do molecular modeling so there have to be rules.  I accept that a fair amount of stupidity may be in play on my part.

Thanks for your consideration,

Mark

[FeLiXe]

are you talking about molecular modeling or just drawing structure formulas?

[Yggdrasil]

In general, chemical structures written on paper do not reflect the actual three dimensional structure of the molecules.  Some representations try to do so, but with complex molecules it is very difficult to do so.

Still, because molecules are three dimensional entities, one must still represent three dimensional information in the two dimensional structures on paper.  One important feature in chemistry is chirality.  Chiral molecules have specific three dimensional arrangements of atoms which create an object what is not superposable on its mirror image.  For example, your right hand is the mirror image of your left hand, but you cannot superpose the two.  However, with a simpler object, say a box or a pencil, the object and its mirror image are exactly identical.

Anyway, to represent the three dimensional arrangement of atoms about a central atom, chemists draw a wedged bonds.  For example, in the image below, the solid wedge indicates that the Br is coming out of the plane of the page and the dashed wedge indicates that the methyl (CH₃) is going into the plane of the page.  The normal lines are in the plane of the page.

Of course, as I said before, these are not accurate representations of the actual structure of these molecules (in addition to being mostly two-dimensional instead of three-dimensional, these drawn structures are also static instead of dynamic), but they do convey all the information chemists need to know to identify and distinguish different molecules.

I hope this answers your question.

[english]

Technically to truly understand the shape and structural integrity of any moleucle would call upon higher orders, such as quantum physics.

As chemists we only consider the nucleus as a particle.  The electrons we treat as particles for the sake of simplicity of a given problem, however they are truly waves in the quantum mechanical sense.


You can consider a particle (nucleus) with wavelike orbitals around the nucleus.  There are sophisticated software programs that do all of the calculations for you, one such is HyperChem. 


Heh, on paper though we stick to whatever visual model works best.  This could vary from Kekule structures to condensed to perspective, Lewis structures or VSEPR/orbital hybridization modeling.  And then there are the molecular orbitals which take calcuations to see, which as aforementioned wouldn't really work out on paper.   


Typically we denote many things by shorthand to designate rather complex things.  A simple   "—" for example denotes a bond.  A "+" or "-" denotes a charge.  The symbol of the particular elemental atom we are referring to is usually used to designate the nucleus.  Dots such as ":" designate electrons.  Moreover we have methods for designating the 3-dimensionality of the structural integrity of these bonds.  Bold-font lines designate bonding electrons coming out of the 2-dimensional plane, whereas light lines (more modernly used as a series of dashes) designate bonding electrons going into the 2-dimensional plane.

There are many, many other methods for designating the sheer complexity of many large molecules, specifically bioorganic molecules.  Yggdrasil would know more about this kind of thing.

[markartist]

Thank you for the replies.

It appears that there are rules that chemists can follow for diagramming or modeling a molecule.  For example, you indicate a three dimensional bond is to be shown by a wedge and a simple bond by a "_" (as close as I can come with my keyboard).

Is there a source for all (or many) of the rules for any given schema of diagramming or modeling?  I have only come to this forum after much effort trying to find the information in other ways.  Ways such as looking in chemistry text books, searching databases, and consulting with research librarians (although not a chemist's library).  I don't have the technical library access that I used to.

Again, my thanks,

Mark