Chemistry

The different Types of Molecular Structures



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If you take an introductory chemistry class, you will no doubt memorize a list of shapes that correspond to particular combinations of lone pairs and bonds around a central atom. Very simple molecules can be classified this way, and based on geometries one can predict the polarity of the molecule. Thinking of molecules in this way is knows as using VSEPR( valence shell electron pair repulsion) theory. The following link provides a nice tutorial so you can correctly answer test questions.

http://www.chem.ox.ac.uk/vrchemistry/vsepr/intro/vsepr_splash.html

Organic chemists, biochemists, and actually most inorganic chemists, don't have it quite so easy. Organic molecules tend to be very large, so one cannot designate one atom as "central". The number of possible shapes is limitless. Biomolecules like proteins and carbohydrates are even larger. A random link from Google mentions protein that has around five hundred atoms, not including hydrogens.

That's not say shapes are unimportant, or even too complex to be studied. Biochemists and biologists devote many research hours and dollars to understanding how the shape of a substrate like, say, a protein from a strand of cat hair, interacts with an enzyme, say, one that produces an immune response. By understanding what sorts of proteins will trigger a response, life scientists can gain a better understanding of allergic reactions and hopefully develop better treatments.

If you look at the structures for the necessary amino acids next to the structures for neurotransmitters, you will see similarities. Phenylalanine looks remarkably like dopamine and is in fact its precursor. Tryptophan looks suspiciously like seratonin and is sometimes used in dietary supplements that claim to have similar effects to certain antidepressants. These claims are correct; such supplements will cause headaches and make you feel sick. They will also waste your money. As a chemist, I felt very foolish when I tried a supplement with a tryptophan-like structure and awoke miserable the next morning, having a pounding headache. Of course supplements containing phenylalanine are beneficial and there is no reason not to take them. By understanding structures of organic molecules, you can make reasonable health decisions. Sometimes, one glance at a structure is enough to see that a drug or supplement is bad news.

Structure also predicts solubility to some extent. Understanding the structure of a drug compound helps chemists formulate things like gel caps and liquid formulations for injection. Injecting a patient with a "liquid" that contains solid particles would not be a good idea. Not only could the solid crystals cause a problem, but the dosage strength would be uneven. My husband works in the pharmaceutical industry and has a better understanding of structure than most of his colleagues. He can often save a lot of time by ruling out formulations that will be unlikely to work.

Other chemical manufacturers use the same principles to make paints, cleaners, glues, and cosmetics. Chemistry is still a poorly understood and therefore very empirical field of study, biology even more so. It is necessary to experiment and test various formulations for safety and effectiveness. However, by having a solid understanding of how a molecule's structure relates to its properties, chemists can move forward with some sense of direction instead of groping blindly.

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