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2: Introduction to Organic Structure and Bonding II

Chapter 2 now matches the updated (2016) edition of Organic Chemistry With a Biological Emphasis.   A complete 2016 edition of the book is available here as a free PDF download.


What does Moby Dick have in common with train engines and skin cream?

“Towards thee I roll, thou all-destroying but unconquering whale; to the last I grapple with thee; from hell's heart I stab at thee; for hate's sake I spit my last breath at thee. Sink all coffins and all hearses to one common pool! and since neither can be mine, let me then tow to pieces, while still chasing thee, though tied to thee, thou damned whale! THUS, I give up the spear!" The harpoon was darted; the stricken whale flew forward; with igniting velocity the line ran through the grooves;--ran foul. Ahab stooped to clear it; he did clear it; but the flying turn caught him round the neck, and voicelessly as Turkish mutes bowstring their victim, he was shot out of the boat, ere the crew knew he was gone. Next instant, the heavy eye-splice in the rope's final end flew out of the stark-empty tub, knocked down an oarsman, and smiting the sea, disappeared in its depths.

Herman Melville, Moby Dick

In the classic 19th century novel 'Moby Dick', Herman Melville's Captain Ahab obsessively hunts down the enormous albino sperm whale which years before had taken one of his legs, the monomaniacal quest ending with Ahab being dragged by the neck to the bottom of the sea by his enormous white nemesis. It is fitting, somehow, that one of the most memorable fictional characters in modern literature should be a real-life 50 ton monster – sperm whales are such fantastic creatures that if they didn't in fact exist, it would stretch the imagination to make them up. They are the largest predator on the planet, diving to depths of up to three kilometers and staying down as long as 90 minutes to hunt the giant squid and other deep-dwelling species that make up the bulk of their diet.

It would be hard for anyone to mistake a sperm whale for any other creature in the ocean, due to their enormous, squared-off foreheads. It is what is inside this distinctive physical feature, though, that brought them to the edge of extinction in the middle of the 20th century. For over 200 years, sperm whales had been prized by whalers for the oil that fills the 'spermaceti' and 'melon' compartments which make up the bulk of the front part of their bodies. Whalers in the 17th and 18th centuries would lower one of their crew into a hole cut into a captured whale, and he would literally ladle out the 'sperm oil ' by the bucketful, often filling eight barrels from the head of one animal. The different processed components obtained from raw sperm oil had properties that were ideal for a multitude of applications: as a lubricant for everything from sewing machines to train engines, as a fuel for lamps, and as a prized ingredient in cosmetics and skin products.

'Sperm oil' is not really an oil – it is mostly liquid wax. The composition of waxes in sperm oil is complex and variable throughout the life of the animal, but in general contains waxes with saturated and unsaturated hydrocarbon chains ranging from 16 to 24 carbons.

Remarkably, scientists are still not sure about the function of the enormous wax-filled reservoirs in the sperm whale's forehead. The most prevalent hypothesis holds that they play a role in echolocation. In the pitch-black void of the deep ocean a whale's eyes are useless, but it is able to navigate and locate prey in the same way that a bat does, using the reflection of sound waves. In fact, the sonic clicks generated by the sperm whale are the loudest sounds generated by any animal on earth. The wax reservoirs may be used somehow for the directional focusing of these sound waves.

Another intriguing but unproven hypothesis is that the reservoir serves as a buoyancy control device. The wax is normally liquid and buoyant at the whale's normal body temperature, but solidifies and becomes denser than water at lower temperatures. If the diving whale could cool the wax by directing cold seawater around the reservoir and restricting blood flow to the region, it could achieve negative buoyancy and thus conserve energy that otherwise would be expended in swimming down. When it needs to return to the surface, blood could be redirected to the wax, which would melt and become positively buoyant again, thus conserving energy on the upward trip.

Whatever its natural function, it is inarguable that the physical and chemical properties of sperm oil make it valuable, both to the whale and to humans. Fortunately for the world's population of whales, both economic forces and conservation efforts have made virtually all trade in sperm oil a thing of the past. Beginning in the late 19th century, the discovery of new oil fields and advances in petroleum processing led to the use of cheaper mineral oil alternatives for many of the major applications of sperm oil, one of the most notable substitutions being the use of kerosene for lamps. More recently, the 'oil' from the Jojoba plant, a native of the American southwest, has been found to be an excellent substitute for sperm oil in cosmetics and skin products, exhibiting many of the same desirable characteristics. Jojoba oil, like sperm oil, is composed primarily of liquid waxes rather than actual oils, and a major selling point of both is that the oily substance produced by human skin, called sebum, is also composed of about 25% wax.

While organic and biological chemistry is a very diverse field of study, one fundamental question that interests all organic chemists is how the structure of an organic molecule determines its physical properties. To understand why sperm oil has properties that made it both a useful industrial lubricant for humans and an effective buoyancy control and/or sonic lens for a hunting sperm whale, we first have to understand the nature of both the forces holding each wax molecule together – the covalent single and double bonds between atoms – and also the forces governing the noncovalent interactions between one wax molecule and all the others around it – the so-called 'intermolecular forces' which determine physical properties such as viscosity, melting point, and density.

That is what we will learn about in this chapter. First, we will look more closely at the nature of single and double covalent bonds, using the concepts of 'hybrid orbitals' and 'resonance' to attempt to explain how orbital overlap results in characteristic geometries and rotational behavior for single and double bonds, as well as bonds that have characteristics of somewhere in between single and double. Then we will move on to a review of the noncovalent interactions between molecules - Van der Waals, ion-ion, dipole-dipole and ion-dipole interactions, and hydrogen bonds - and how they are manifested in the observable physical properties of all organic substances.

Before reading any further on this chapter, you will probably need to go back and review some topics from your Introductory Chemistry course. Be sure that you understand the concepts of atomic orbitals, atomic electron configuration, and that you are able to describe s and p orbitals and orbital lobes and nodes. Now would also be a very good time to review VSEPR theory. You might want to watch review tutorials from Kahn academy on atomic orbitals and electron configuration and dot structures and VSEPR theory.