CHAPTER 1
Fundamental Models of Organic Chemistry

1.1 ATOMS AND MOLECULES

Basic Concepts

Organic chemists think of atoms and molecules as basic units of matter. We work with mental pictures of atoms and molecules, and we rotate, twist, disconnect, and reassemble physical models in our hands.1,2 Where do these mental images and physical models come from? It is useful to begin thinking about the fundamental models of organic chemistry by asking a simple question: What do we know about atoms and molecules, and how do we know it? As Kuhn pointed out,

Though many scientists talk easily and well about the particular individual hypotheses that underlie a concrete piece of current research, they are little better than laymen at characterizing the established bases of their field, its legitimate problems and methods.3

Much of what we know in organic chemistry consists of what we were taught. Underlying that teaching are observations that someone has made and someone has interpreted. The most fundamental observations are those that can be made directly with human senses. We note the physical state of a substance—solid, liquid, or gas. We see its color or lack of color. We observe whether it dissolves in a given solvent and whether it evaporates if exposed to the atmosphere. We might get some sense of its density by seeing it float or sink when added to an immiscible liquid. These are qualitative observations, but they provide an important foundation for further experimentation.

It is only a modest extension of direct observation to the use of some simple experimental apparatus for quantitative measurements. A heat source and a thermometer allow determination of melting and boiling ranges. Other equipment allows measurement of indices of refraction, densities, surface tensions, viscosities, and heats of reaction. Classical elemental analysis indicates the elements present in a sample and their mass ratios. In all of these experiments, the experimenter uses some equipment but still makes the actual experimental observations by eyes. These simple techniques can provide essential data, nonetheless. For example, finding that 159.8 grams of bromine will always be decolorized by 82.15 grams of cyclohexene leads to the law of definite proportions. In turn, that suggests a model of matter in which submicroscopic particles combine with each other in characteristic patterns, just as the macroscopic samples do. It is then only a matter of definition to call the submicroscopic particles: atoms or molecules. It is essential, however, to remember that laboratory experiments are conducted with materials. The chemist may talk about the addition of bromine to cyclohexene in terms of individual molecules, but that can only be inferred from experimental data collected with macroscopic samples of the reactants.

Electronic instrumentation opened the door to a variety of investigations that expand the range of observations beyond those of the human senses. These instruments extend our eyes from seeing only a limited portion of the electromagnetic spectrum to detecting practically the entire spectrum, from X‐rays to radio waves, and they let us “see” light in other ways (e.g. in polarimetry). They allow us to use entirely new tools, such as electron or neutron beams, magnetic fields, and electrical potential or current. They extend the range of conditions for studying matter from near atmospheric pressure to high vacuum or high pressure. They effectively expand and compress the time scale of the observations, allowing study of events that require eons or that occur in zeptoseconds.4,5,6

The unifying characteristic of modern instrumentation is that we no longer observe the chemical or physical change directly. Instead, it is detected only indirectly, such as through changes in pixels on a computer display. With such instruments, it is essential to recognize the difficulty in freeing the observations from constraints imposed by expectations. To a layperson, a UV‐vis spectrum may not seem very different from an upside‐down infrared spectrum, and a capillary gas chromatogram of a complex mixture may appear to resemble a mass spectrum. But the chemist sees these images not as lines on a paper or a computer display but as vibrating or rotating molecules, as electrons moving from one place to another, as substances separated from a mixture, or as fragments produced in a mass spectrometer. Thus, implicit assumptions about the origins of experimental data both make the observations interpretable and influence the interpretation of the data.7

With that caveat, what do we know about molecules and how do we know it? The first assumption is that all substances are composed of atoms—indivisible particles that are the smallest units of that particular kind of matter that still retain all its properties.8 As noted, it is convenient to correlate observations that substances combine only in certain proportions with the notion that these submicroscopic entities called atoms combine with each other only in certain ways.

Much fundamental information about molecules has been obtained from spectroscopy.9 For example, a 4000 V electron beam has a wavelength of 0.06 Å, so it is diffracted by objects larger than that size.10 Interaction of the electron beam with gaseous molecules produces characteristic circular patterns that can be interpreted in terms of molecular dimensions.11 We can determine internuclear distance through infrared spectroscopy of diatomic molecules and can use X‐ray or neutron scattering to calculate distances of atoms in crystals.

“Pictures” of atoms and molecules may be obtained through atomic force microscopy (AFM) and scanning tunneling microscopy (STM).12,13 For example, investigators reported images of pentacene that displayed individual atoms,14 polycyclic aromatic hydrocarbons that allowed determination of bond order,15 products of single‐molecule chemical reactions,16 molecule‐gears,17 and a video of a single fullerene molecular shuttling in a vibrating carbon nanotube.18 Investigators also reported visualizing atomic orbitals,19 imaging the lateral profiles of individual sp3 hybrid orbitals, and determining the electronegativity of individual surface atoms.20,21 AFM was used to characterize the strength of intermolecular hydrogen bonds.22 Some investigators reported imaging single organic molecules in motion with transmission electron microscopy,23 and others reported studying electron transfer to single polymer molecules with single‐molecule spectroelectrochemistry.24

Even though “seeing is believing,” it is important to remember that these experiments do not really show molecules—just computer graphics. Some examples illustrate this point: STM features that had been associated with DNA molecules were later assigned to the surface used to support the DNA.25 An STM image of benzene molecules was reinterpreted as possibly showing groups of acetylene molecules instead.26 AFM images suggesting the visualization of intermolecular hydrogen bonds were questioned when it was shown that similar images could be observed when such hydrogen bonding should not be possible.27,28

Organic chemists also reach conclusions about molecular structure on the basis of logic. For example, the fact that one and only one substance has been found to have the molecular formula CH3Cl is consistent with a structure in which three hydrogen atoms and one chlorine atom are attached to a carbon atom in a tetrahedral arrangement. If methane were a trigonal pyramid, then two different compounds with the formula CH3Cl might be possible—one with chlorine at the apex of the pyramid and another with chlorine in the base of the pyramid. The existence of only one isomer of CH3Cl does not require a tetrahedral arrangement; however, since there could also be only one isomer if the four substituents to the carbon atom were arranged in a square pyramid with a carbon atom at the apex or in a square planar structure with a carbon atom at the center. Since no one has identified more than one CH2Cl2 molecule, the latter two geometries seem unlikely. Therefore, the parent compound, methane, may be tetrahedral as well. This view is reinforced by the existence of two different structures (enantiomers) with the formula CHClBrF. Similarly, we infer the flat, aromatic structure for benzene by noting that there are three and only three isomers of dibromobenzene.29

Organic chemists do not think of molecules only in terms of atoms, however. We often envision molecules as collections of nuclei and electrons and consider the electrons to be constrained to certain regions of space (orbitals) around the nuclei. Thus, we interpret UV‐vis absorption and emission spectroscopy in terms of movement of electrons from one orbital to another. These concepts resulted from the development of quantum mechanics. The Bohr model of the atom, the Heisenberg uncertainty principle, and the Schrödinger equation laid the foundation for current ways of thinking about chemistry. Although there may be some truth in the statement that

The why? and how? as related to chemical bonding were in principle answered in 1927; the details have been worked out since that time.30

there are still uncharted frontiers of those details to explore in organic chemistry.