Sunday, March 1, 2009

Organic Chemistry, Chapter 1

Young Grasshopper, sit with me awhile here near the mountaintop, and ponder the greater meaning of things. The sound of the wind, the rustle of leaves, and the babbling stream harbor great wisdom if we may quiet ourselves and listen to what they may have to tell us. My young student, I would also advise against rapid adjustment of your loincloth, as it might result in an embarrassing accident. There, let us be seated, and find a subject for our reflection. Let us ponder the brook, here. See how its water flows! It needs no direction, no master to know how to move. It has no map, yet as sure as we are sitting here, we may know that it shall find the sea! What a strange phenomenon, that a drop of water, or a flake of snow, which will fall upon this mountaintop will contain within it all that it needs to make such a long, long journey. Close your eyes, and meditate with me for a spell, about this running brook, and how it makes its way. Concentrate. Focus. Leave your material body behind. Rise up, away from the mountain. What do you see? See how the water flows, moving from the place which is higher to the place which is lower always taking the path which is leading it downward. You may perhaps have heard that things which are “higher” tend to move to be “lower,” and that this is the result of some quantities called energies, which we yet cannot see, but we are asked to believe that they must be there. Were you satisfied with this explanation? Perhaps not. That is because this is only the smallest part of the story. Let us see if we can now find more. What is that you ask? Will this be on the exam, and what has this to do with chemistry? Hmmm… You seem to be overly concerned with the material cares of this world. They dominate your consciousness, but you will only become great if you can let them go. Yes, this will be on the exam. Concentrate, young Grasshopper. There is much you have yet to learn. Pull yourself further away, further and further, till the mountain is just a speck, and the curvature of the earth is now visible. Move further away, till the whole world is in view, but fix your mind always on that same little brook, flowing beside that material body you have now left behind. Now I ask you: which way is higher, and which lower, which is up and which is down? Ha! Now we see that these directions are an illusion, dependent upon our frame of reference, and greater understanding might be available if we might begin to ponder from this new vantage point: What is the objective of movement now? Let us seek the answer. Using the power of your mind, reach out with your hand, and gently turn the globe, until our mountaintop is silhouetted against the sky and the blackness of space, and the little stream flows to form an outline between that mountaintop and the sky above. See how the stream moves almost laterally along the surface, searching its way to fill in any “holes” or “depressions” it may find, pooling here and there, until finally making its way to the biggest “hole” it might ever find: the sea itself, where it appears to be satisfied, until displaced by the sun and the winds to some new mountaintop to begin the journey anew. Why such behavior? Why, indeed, do “holes” need filling, and why should a planet desire to be so smooth? Why are the celestial bodies round? Only now do we begin to see the “shape” of our answer. For as the countless particles which form the bodies that make up the universe arrange themselves, guided as they are by the force of gravity upon each and every one of them, they seek a specific shape: the sphere. For the sphere provides what no other shape can: a minimization of the distance between bodies mutually attracted to one another. As we can now plainly see, water flows to the sea for one very simple purpose: because doing so will make the world more round. And we can now understand a simple but profound law: all objects mutually attracted to one another will seek to minimizes the distance between them. The earth, the water, the sky, all arrange themselves to minimize the displacement of mass, the dense in the middle, the light at the surface, to form our world. My young student, as it is with the world, so is it with chemistry. As mass is attracted to mass, so is charge to opposing charge. Ponder now the first row of the periodic table. As we move from left to right, the charge of the nucleus must increase, yet the shell of the electron remains the same. As we might expect, with each succeeding proton, the cloud of electrons draws nearer, ever more attracted as it is to the increasingly positive charge at the nuclear core. Thus do atoms become smaller, from boron to carbon to nitrogen to oxygen to fluorine. Likewise, as the electron pines for its counterpart, the proton, once free to roam about, it shall inevitably seek to nestle in closely as it can to the positive charge of the smaller atoms, just as the river pines for the sea, proximate as it shall ever be to the earthen core. Thus do elements at the right of the table draw electrons more strongly than those to the left of the table. This ability to attract electrons is termed electronegativity. Do you understand this lesson which we have learned together? Let us consider a few questions: Firstly, considering an electron confined to an orbital of the following shapes, which will be the preferred orbital, and in what order will they be filled? Naturally, the order is s, p, d, for this is the order of increasing displacement from the nucleus, from least to greatest. Secondly, considering orbitals of a hybrid nature, which shall be the order of preference? Once again, it shall be s, sp, sp2, sp3. For exactly the same reason. Ponder with me, given that a bond is to be formed between two atoms, say, carbon and oxygen, where are the electrons to reside? Of course! The electrons shall show favor to the element oxygen, as it has the higher nuclear charge and the smaller radius. Thus we may understand the buildup of negative charge along the length of a bond, and the origins of the phenomenon of bond polarization: A bond between atoms of differing negativity is said to be more polar than a bond between atoms of similar electronegativity. Now, to begin to see the way of electron flow, as it occurs in the universe, and the basis of the subject we call chemistry: Given the following two arrangements of atoms and their bonding, which arrangement will be favored? The carbon shall be bonded to oxygen, as this is the arrangement that minimizes the distance between electrons and positive charge. With respect to our metaphor, this arrangement is “more round,” and as a general rule, more polar bonds are energetically favored over less polar bonds. Now, young Grasshopper, we shall examine your understanding. See if you may answer the following, on your own. Question 1: Which of the following substances might burn in an atmosphere of oxygen? Oxygen, being elementally pure in its makeup, would contain only bonds to other oxygen atoms. Question 2: Among the compounds listed below, two are explosives. Choose them, and explain carefully what structural features make them explosive. Question 3: Which proton (a hydrogen atom nucleus) shall be easier to remove from the carbon atoms of the following pair, and why? Have you meditated long enough? Do you have your answers? We shall see.... Question 1: Aluminum powder and CH4 (methane, or natural gas) are flammable, while the other two are not. Aluminum, and most other pure elements, will oxidize ("burn") in an oxygen atmosphere. If the element is pure, its electrons are necessarily shared equally in any bonds between atoms. Oxygen has a higher electronegativity than most other elements, and therefore its bond with another element will almost always allow the electrons involved to locate themselves closer to nuclear charge, relative to each element in its pure form. Aluminum powder is used as a solid rocket fuel booster. In the case of methane, this is not a pure element, but we are told that the two elements involved have similar electronegativity, so that the electrons are roughly symmetrically distributed within the bonds. By rearranging to form bonds with oxygen, the electrons will be able to draw nearer to the oxygen nucleus, thus achieving a lower energy state. HOH is probably more familiar as water. Since hydrogen is already bonded directly to oxygen, it is not possible to achieve a lower energy state through rearrangement. It is already in a very stable state. So water, even though it is composed of hydrogen and oxygen, is not flammable. NaCl, table salt, is composed of elements from opposite sides of the periodic table. Its bonds are already quite polar, and rearrangement with oxygen will not achieve significant movement of electrons to an energetically more favorable position. So NaCl is not flammable. (Sodium and chlorine in their pure states, on the other hand, are capable of some very "exciting" chemistry!) Question 2: The first and fourth compounds, acetone peroxide (Mother of Satan) and trinitrotoluene (TNT), are explosive. Isopropanol, sodium hydroxide, and benzene are not, although isopropanol and benzene are both flammable in oxygen. Both the explosive molecules contain bonds between relatively electronegative atoms (oxygen-oxygen bonds and nitrogen-oxygen bonds) as well as bonds between atoms of relatively low electronegativity (carbon-carbon and carbon-hydrogen bonds). Thus they can spontaneously rearrange to produce much more stable bonds between atoms of widely differing electronegativity (carbon-oxygen, hydrogen-oxygen, etc.), releasing energy and forming gasses in the process. Isopropanol contains a mixture of different elements, but in particular, the oxygen atom already has two very polar bonds. There is no way to rearrange atoms to generate a bonding pattern that is particularly more energetically favorable. Likewise with benzene and sodium hydroxide, because all the atoms are low-electronegativity (benzene), or the bonds are already all very polar (sodium hydroxide) there is no available path to a significantly lower energy bonding arrangement. Question 3: Removing the proton (hydrogen nucleus) bonded to carbon leaves an electron pair on carbon without a bonding partner. A lot of energy will be required to separate the two charges which are attracted to one another. In the case of the sp hybridized carbon, however, the electrons are drawn closer to the nucleus of carbon than in the case of the sp3 hybrid carbon. So, relative to the sp3 example, they will be more stabilized, and this carbon will be easier to "deprotonate." Generally speaking, an sp hybridized C-H bond is more acidic than an sp hybridized C-H bond. There are exceptions, however. Congratulations! You are well on your way to becoming a Master of Organic Chemistry!


  1. I guess I'm grateful I remembered all that. (Of course, I'm old; when I was studying chemistry there were only 14 elements.) But I have to admit, I would have learned it a lot more easily with this kind of instruction.

  2. Well Scott if you could relate economics to organic chemistry I might have a better chance of understanding of our current economic state. Currently, I feel like a first day organic student reading this post, when I try your others, but I am trying.

    I am trying a project that may work for economics. I currently label my clothing as various atoms so I know which are 'compatible'. This avoids asking my wife which items match, or getting the comment as I walk out the door "You're not going to wear that, are you!?"

    Good to see you getting back to your roots, but what brought on such a random (but very enlightening) post?