A (3D) Model Education

December 28, 2008 11:03 AM

ChemistryFilter: How can I use a molecular model that was given to me to learn about the wonders of chemistry?

I was given a molecular model set for Christmas.

Basically, I have a strong interest in chemistry/biochemistry, and hope that I can go through some exercises with this set to learn more about chemistry.

Any ideas?

I would love to be able to become better at "picturing" certain molecules, bonds, etc.

My chemistry knowledge is quite basic so I have a lot to learn. Even small things have helped thus far. For example, I made a model of ethyl alcohol and it really put into perspective just as to why some atoms are terminal and why some aren't.

Thanks!

posted by PaulingL to science & nature (9 comments total)

get an organic chemistry book, that model will help you visualize what you're learning.
posted by Large Marge at 11:25 AM on December 28, 2008

Models are great for understanding chirality, the "handedness" of molecules. Two-dimensional representations of molecules sometimes incorporate clues indicating that certain bonds are above or below the plane of the paper, but even those can be hard to visualize. Most of the time, these clues are not used even if the chirality of the molecule is important.

Many molecules of great importance in biology are chiral, and enzymes usually recognize one enantiomer but not the other. Amino acids and sugars are chiral, just to give a couple of examples.

An interesting thing about chirality is that most of the time in the lab, it doesn't matter. Most analytical methods can't distinguish one enantiomer from another, and chemists have to use very specific methods to analyze and/or separate them.

Biology is the big exception, though - chirality affects almost everything here, because we are built of chiral molecules ourselves. Smell and taste often depend on chirality: the classic example is carvone, whose S-(+) isomer smells like caraway, and whose R-(-) isomer smells like spearmint. Stereochemistry is also important in drug design. For example, cisplatin is a useful albeit toxic chemotherapy drug, but transplatin, the other stereoisomer, is toxic but useless.

Build yourself a model of a couple of stereoisomers. Note how different they feel when you hold them in your hands (because your hands are "handed"), even though the structures look so similar when drawn on paper. Explore the difference between chiral and nonchiral molecules, and chiral versus nonchiral atoms within chiral molecules. This is the best use for chemical models in my experience - even computer graphics depicting molecules don't give you the same feel (literally!) for chirality.
posted by Quietgal at 12:31 PM on December 28, 2008

Is that the only portion of chemistry it would be applicable to? I am currently enrolled in the second semester of general chemistry as well as analytical chemistry.
posted by PaulingL at 12:31 PM on December 28, 2008

Molecular models can be applied to any chemical discipline (however there are some that are mainly geared towards organic). The best thing to to would be to model all the molecules you study in your courses.
posted by stevechemist at 1:10 PM on December 28, 2008

No, it's very much applicable to analytical chemistry as well - in my undergraduate labs, for example, identifying stereoisomers was part of several experiments. And I'd like to disagree a little with what Quietgal said: if you're doing theoretical organic chemistry (writing reactions on paper), many reactions do create products with predictable stereochemistry, and people will care about it. Furthermore, because so much of orgo these days is directly or indirectly related to biochemistry (or drug design), it's not something most chemists can afford to ignore.

A basic modelling kit won't be very useful for dealing with metals (inorganic chemistry) - once you get into dealing with the f orbitals, things get too complicated for a simple kit to handle. (That doesn't mean that stereochemistry isn't important for inorganic chemistry, though, or that the things you learn by studying stereochemistry in inorganic systems will be inapplicable! You just won't be able to easily and directly model it.) A modelling kit won't be very useful for physical chemistry either, which is the most physics-like end of chemistry. But for everything else, understanding stereochemistry is very definitely important!

A good basic orgo text - McMurry's "Organic Chemistry" is the one I used - will help you make sense of stereochemistry and how it affects reactions, while a basic biochemistry text - I used "Biochemistry" by Voet and Voet - will give you a good idea of why proteins and other biomolecules are so sensitive to stereochemistry. It's a great idea to model the reactants and products in a given reaction, or any structure that seems confusing to you.
posted by ubersturm at 1:13 PM on December 28, 2008

Oh, heck no. You can use models to help you see and understand many aspects of molecular structure. Like why saturated fats tend to be solid at room temperature whereas unsaturated fats are usually liquid: the fatty acid chains with all C-C single bonds are straight and pack easily into sorta-crystalline solids, while the chains with double-bonds have kinks that resist packing neatly into solids. No chirality here, just straightforward geometry.

As for stereochemistry, it eventually crops up just about everywhere. It's a pain in the butt since it's hard to represent 3D molecules on 2D paper, so chemists tend to ignore it if they don't absolutely have to deal with it. (It's also hard for left-brained people like me to think in 3 dimensions, and I never really grokked stereochemistry so I mostly try to ignore it.) But at some point you'll have to deal with it. Even in general chemistry you'll touch on it since it's a fundamental principle, not restricted to organic compounds (although vastly more common in the world of carbon).

Not so much in analytical chemistry, since as I said, most analytical techniques are blind to chirality and most chemists don't want to bother with it unless they really have to. But you might do a few lab exercises in chiral separations; there are HPLC columns that can resolve certain enantiomers. And there's always the classic spectroscopic technique of passing a beam of polarized light through a chiral solution and seeing which way the beam is rotated (the first observation of chirality, in fact).

If you continue on to organic chemistry, that's where you'll see stereochemistry as a big topic. And of course biochemistry is full of chiral molecules so you'll get more stereochemistry than you ever wanted (if you're like me, that is). By the way, your username has a chiral connection: Vitamin C is the L-enantiomer of ascorbic acid. There's just no escaping that bothersome chirality!
posted by Quietgal at 1:20 PM on December 28, 2008

If you're going to have a modelling kit, I would recommend Kirby's Stereoelectronic Effects, which is a tiny little book, more like a pamphlet really, that talks about how the placement of orbitals in space guides reactions.
posted by d. z. wang at 1:28 PM on December 28, 2008

Model kits help with certain things (calculating energy penalties on cyclohexane, whee), and somewhat for stereo stuff, but really when you start hammering away at learning organic chemistry you start getting a feel for how things exist in 3d, what the bond angles are going to be, when a reaction will be sterically hindered or not. A lot of that stuff, it may be helpful to have a model example once, but after that the representation on paper is enough. Stereochemistry is a drag, but if you're just trying to think about it, and not trying to preserve or target it, it's not that bad - again, the models help the first time, but the 2d representations really aren't bad. I took 4 quarters of organic chemistry, but I am not a chemist, and so these views may only hold for intro chem.
posted by devilsbrigade at 3:43 PM on December 28, 2008

Sorry to bring back an old topic, but for the record, a molecular kit is excellent for symmetry in chemistry. Working out the point groups and symmetry operations in molecules become a lot easier. Suddenly, using Huckel theory to find secular equations ain't as bad as it seems!
posted by dragontail at 11:41 AM on March 1