Organic Chemistry


MODULE #1 Organic chemistry as 3D Art


REPRESENTATIONS of 3D objects (including organic molecules) using only 2D drawings can be confusing. Practice constructing and interpreting these drawings. Work to UNDERSTAND what the drawings are telling us!

Methane --- not as simple as it seems?

Consider the simplest hydrocarbon, methane, whose molecular formula is CH4. For the beginning student, it is sometimes easy to forget what this simple formula actually represents. A molecule of methane is comprised of one carbon atom and 4 hydrogen atoms, but how are these atoms connected? What geometry characterizes the complete molecule?

Because the carbon has four electrons available for bonding and each hydrogen can contribute a single electron to bond formation, the 5-atom molecule consists of a central carbon atom attached to each of 4 IDENTICAL hydrogen atoms by 4 EQUIVALENT single covalent bonds.

Although all bonds and all hydrogens within this molecule are completely equivalent, they are often represented in ways that tempt us to view them as non-equivalent. Work to get comfortable with the fact that ALL of the following are equivalent and acceptable representations of the methane molecule.


Methane --- giving depth to our understanding

These drawings do an adequate job of representing the equivalency of the four hydrogens and the four associated bonds to the central carbon atom of the molecule, but NONE of the drawings convey the 3D character of this simple molecule. From the representations above, you could quite reasonably expect that the methane molecule has a planar structure with all five atoms (one carbon and four hydrogens) and all four bonds in a single plane. Such is not the case. The actual geometry of the methane molecule has been DETERMINED EXPERIMENTALLY to be tetrahedral. That is, each of the four hydrogens is known to occupy a position at the apex of a regular tetrahedron with the carbon positioned at the center of that tetrahedron. This bonding geometry around carbon exists in all of the simple hydrocarbons and has been EXPLAINED THEORETICALLY on the basis of what's known as "orbital hybridization"…more about that in another module.

In an effort to improve the utility of our 2D drawings in representing molecules that are 3D in real-life, we can take a couple different approaches. In either case, the concept is to remind ourselves that although various bonds within molecules may be chemically equivalent, they may at the same time, be spatially distinct. Probably the most common approach involves the use of dashed and solid wedges. Since any three objects (atoms in this case) will determine a plane, you can choose the carbon and any two of the four hydrogens to define an arbitrary plane…most conveniently the plane of your monitor's screen. Because of the overall 3D tetrahedral geometry of the molecule, the remaining two carbon-to-hydrogen bonds will be oriented in opposing directions relative to that plane. One will be projecting out from the screen (symbolized by a solid wedge) and the other will be projected back into your monitor (symbolized by a dashed wedge). Notice that the bonds lying IN the arbitrary plane are drawn in the normal fashion. Work on your ability to relate this type of representation to the actual 3D structure of the molecule.


Recognizing that any of several equivalent viewpoints (the perspective from which we view the molecule) could have been chosen for this representation, a number of chemists have proposed various standardized viewpoints to be assumed in describing these 3D geometries. Two of the most widely recognized standards are the Fischer projection and the Newman projection.

In the Fischer projection, the molecule is viewed so that all of the bonds to the central carbon appear to be oriented horizontally and vertically with the horizontal bonds projecting toward the viewer and the vertical bonds projecting away from the viewer. Use of this standardized viewpoint eliminates the need to include dashed or solid wedges in the drawing, but only because it is understood that the molecule is NOT planar, and the bonds project according to convention.


A Newman projection involves a viewpoint that superimposes the viewers' line of sight with the axis of one of the bonds to the central carbon atom. The central carbon terminus of that bond is always oriented closest to the viewer, and the projection diagram represents the remaining three hydrogens as they protrude toward the viewer from that carbon (represented as a large circle).


What happened to the fourth hydrogen? Did it get lost in this process? Not at all…it's there…you just can't see it because it's hidden from view by the carbon in front of your nose!

Methane derivatives --- replacing some of the hydrogens

Consider next the molecule resulting from the substitution of ONE hydrogen in methane with a single bromine atom --- we can call it bromomethane or methyl bromide. (Much to the chagrin of new students of organic chemistry, many of the simpler molecules have both "systematic" names and "common" names…you should familiarize yourself with both, but we will always mention the systematic name first.) We will need to specify which of the hydrogens will be substituted by the bromine, and you might expect the best choice of product to be found among the following…


And you would be correct, regardless of your choice of representation!!! That's because we said earlier that methane has only ONE TYPE of hydrogen, and if a single bromine is substituted for any given hydrogen, the resulting molecule will be indistinguishable from that resulting from substitution of any other hydrogen. A molecule containing only ONE TYPE of hydrogen will yield only ONE product of mono-substitution…in other words, ALL of the diagrams above are equivalent representations of the same molecule. The 3D representations may make it more apparent that only a single product is possible:


Now consider a second substitution, this time with a single chlorine atom replacing one of the three remaining (indistinguishable) hydrogens of the bromomethane molecule. We will name this product bromochloromethane (with two substituents on the parent methane, they are listed alphabetically). Again our 3D representations make it clear that only one di-substituted product is possible, even though we may choose to view the molecule from any of a number of different perspectives:


You might want to draw other arrangements of these atoms to convince yourself that no matter which two hydrogens are chosen for substitution, only ONE bromochloromethane product is possible. No matter where you position the bromine and chlorine in your initial drawing, you will always be able to rotate or flip the drawing to give you the same representation as shown above; you will always be able to superimpose your drawing on the one above because both describe only a single product.

Methane derivatives --- replacing all but one hydrogen

Further substitution with a third halogen atom, like iodine to produce bromochloroiodomethane, makes things interesting. Using the dashed-and-solid wedge method to describe the 3D geometry for this molecule, compare the results of substitution for either of the remaining hydrogens of bromochloromethane:

[Tipped & Turned][Tipped & Turned]


Are these two different perspectives of the same product, or are there two different products in this case? After examining these molecules from the various perspectives, you should be convinced that the molecule on the right of the screen is simply the MIRROR IMAGE of the molecule on the left. No matter how you may change your viewpoint of either, they remain NON-SUPERIMPOSABLE, non-identical mirror images. For certain, all objects have mirror images, and many of those objects have mirror images that are indistinguishable from the original object. But other objects, like a molecule of bromochloroiodomethane, have mirror images of the non-superimposable variety; objects of this type are referred to as being CHIRAL. Common objects displaying CHIRALITY include hands, gloves, scissors, feet, shoes, golf clubs, and dice.

For the objects of organic chemistry, the presence of a single carbon bonded to four DIFFERENT substituents will result in a chiral molecule. Consequently, that particular carbon is called a chiral or ASYMMETRIC carbon; it is the center of chirality or asymmetry for the entire molecule. When more than a single chiral carbon is present within the same molecule, the chiral character of the overall molecule may be more complex, and will be discussed in a subsequent section. For purposes of the current discussion however, let it be recognized that for any molecule, regardless of the number of chiral centers within that molecule, if you can identify an internal mirror plane …a plane that divides the molecule into two mirror-image halves…that molecule and its mirror image WILL BE SUPERIMPOSABLE. In other words, the molecule will NOT be chiral even though it may contain individual carbons that are chiral. This is an important point to understand; take the time to be sure you do!!!

What is an isomer?

Use of the prefix "iso-" in conjunction with the names of chemical substances relates to their similarities, rather than their differences. ISOmers are related by having in common the same type and number of constituent atoms or groups of atoms; the distinctions among ISOmeric molecules lie only in the arrangement of those constituents. STRUCTURAL isomers have uniquely different bonding relationships among their various molecular constituents, whereas STEREOISOMERS have identical bonding relationships, but differing spatial orientations of those same constituents.

Chiral molecules come in isomeric pairs referred to as ENANTIOMERS, or as an ENANTIOMERIC PAIR. This specialized type of isomerism is particularly relevant to students of the health sciences because it characterizes the vast majority of chemicals taken into the body (as foods or drugs) as well as those that are produced by the body. All of plant and animal life revolves around molecules and reactions that display an overwhelming preference for only ONE of the members of an enantiomeric pair. Although most biological systems are totally discriminating between enantiomers, conventional laboratory distinctions are seldom observed. Both of the enantiomers will have identical melting points, boiling points, refractive indices, and absorption spectra; conventional reactions will produce identical quantities of each enantiomer. The only physical property that differentiates between enantiomers results from the interaction of these molecules with plane-polarized light. Interaction of ordinary molecules with such light does not effect the plane in which the light is polarized; in other words, the plane of light that emerges from a sample of ordinary molecules will be identical with the plane of light entering that sample. With a sample of ONE isomer of an enantiomeric pair, the plane of the entering light will be rotated as it passes through the sample. The longer the sample path, or the more concentrated the sample solution, the greater the rotation of the emerging light. When the original isomer is replaced with its mirror image isomer, under the same measurement conditions, this sample will cause the light plane to rotate an IDENTICAL amount, but in the direction OPPOSITE to that originally observed. The amount of rotation is reported in degrees and the direction of rotation (as viewed when looking toward the light source) is reported as positive (+) or dextrorotatory (d) when rotated to the right, and negative (-) or levorotatory (l) when rotated to the left. Substances that display this light-rotating property are referred to as being OPTICALLY ACTIVE. Pairs of molecules whose only distinguishing characteristic lies in their interaction with plane-polarized light are called OPTICAL ISOMERS.

Methane derivatives --- naming optical isomers

Each of the two enantiomers of bromochloroiodomethane that were described above requires a name. If we knew the direction of plane-polarized light rotation for one of the isomers, we could add (+) and (-) prefixes or d- and l- prefixes to the names (we would know that the other isomer had the opposite rotation). However, since the rotation is an experimentally determined value, we often don't have immediate access to that information; all we have are the structural drawings of the molecules. Consequently, a method for naming (nomenclature) these substances based only on their 3D representations has been developed. The system may best be understood through use of the Newman projections described previously. The method requires that we first identify all chiral centers of the molecule. Then we prioritize all four substituents that are attached to each center, prioritization being established on the basis of atomic weight. Finally, with the molecule oriented such that the bond between the chiral center and the substituent of lowest priority faces away from us, we look to see if the remaining substituents are arranged in a clockwise (right-handed, rectus, "R") or a counterclockwise (left-handed, sinister, "S") configuration. With the knowledge that the atomic weights of hydrogen, bromine, chlorine, and iodine are approximately 1, 80, 35.5, and 127, respectively, we can uniquely identify the two enantiomeric forms shown below:



Again, the hydrogen is not visible because as the lowest priority substituent, its bond to carbon is oriented away from us and therfore hidden from our view.

Ethane, propane, and butane --- carbon groups as sustituents

With the extension of the methane molecule by one carbon and its associated hydrogens, the C2H6 hydrocarbon known as ethane is obtained. Since the four hydrogens of methane are all equivalent, the replacement of any one of them with this additional carbon group would give the same product --- ethane. The resulting ethane molecule now has six equivalent hydrogens that can each be replaced in the same manner as previously discussed for methane.

Consider the substitution of a single bromine for one of the hydrogens of ethane. Again, even though all of the following figures are drawn differently, they still represent only the single substance known as bromoethane or ethyl bromide.


Looking at the corresponding 3D representations for this molecule may again be helpful in convincing yourself that only one mono-bromide can be produced from ethane.


Now again consider a second substitution, this time with a single chlorine atom replacing one of the remaining hydrogens of bromoethane. What's different this time? For the second substitution with bromomethane that we discussed previously, all remaining hydrogens were equivalent, so it didn't matter which one was replaced. NOT SO with the hydrogens of bromoethane!!! There are TWO distinct TYPES of hydrogen in this molecule…there are the two hydrogens attached to the carbon that is directly bonded to the bromine, and there are the three hydrogens attached to the adjacent methyl group. Two different types of hydrogen…two different types of product from this second substitution. If the chlorine replaces one of the methyl hydrogens, the product is named 1-bromo-2-chloroethane; if one of the other hydrogens is replaced, the product is named 1-bromo-1-chloroethane. Such numbering is commonly used to remove ambiguities in specifying the relative positioning of multiple substituents in a given molecule. Each carbon of the parent chain is numbered in sequence, and the number associated with each substituent refers to the carbon to which that substituent is bonded. The #1 carbon is assigned by a variety of rules which depend on the nature of the particular molecule, and in this case the #1 carbon is the carbon bonded to the first named substituent in an alphabetized list of all substituents of the molecule.

These two different bromochloroethanes illustrate isomerism of another kind…positional isomerism. For these isomers, as the name implies, although the same substituents are present in both molecules, the points of attachment to the main chain are different in each case. Unlike the optical isomers discussed previously, these isomers are easily distinguished by the most common of physical and chemical properties; they have different melting points, boiling points and refractive indices. They are often distinguished by their uniquely different absorption spectra.

Conformations of 1-bromo-2-chloroethane

Examination of the 3D representations of the 1-bromo-2-chloroethane reveals yet another detail to be addressed in describing molecular geometries.


The perspective provided by the Newman projection is most helpful in this regard. Notice that in this representation, carbon #1 is closest to us; carbon #2 is hidden from our view, but we can still see the other atoms that are bonded to that carbon, in this case two hydrogens and a single chlorine. In the particular CONFORMATION shown above, the relative positioning of the bromine and chlorine allows these two larger (relative to hydrogen) substituents to distance themselves from each other by the maximum amount. Compare this to the positioning shown in the two conformations below.


Since the transition from one conformation to another involves only a simple rotation about the single bond connecting the two carbons, these transitions happen easily and continuously. Only under very unusual circumstances (such as very low temperature or very large bulky substituents) can the individual conformations actually be observed or isolated. Nonetheless, it is common to speak of the relative stabilities (energies) of these same conformations. The Newman projections show conformations that are either "staggered", or "eclipsed", and in the absence of other factors, the staggered conformations are the more stable (lower in energy). Because of bulk interactions (steric effects) between groups aligned directly across from each other, and in some cases because of repulsive bond polarities, the eclipsed conformation is generally far less stable. Among the possible staggered conformations, those that minimize steric effects and bond repulsions have the greatest stability, or lowest energy.

Although "isomers" typically display different molecular structures (bonding arrangements) while at the same time sharing a common molecular formula, "conformers" share both molecular structure and formula.

Configurations of 1-bromo-1-chloroethane

Notice anything special about the replacement of one of the remaining two hydrogens on the #1 carbon of bromoethane? With chlorine you will get 1-bromo-1-chloroethane, but is more than one possible??? You bet…the introduction of the chlorine has now produced a carbon with four different groups attached…a hydrogen, a bromine, a chlorine, and a methyl group...that defines a chiral carbon. One chiral carbon means a chiral molecule; a chiral molecule means two non-superimposable mirror-image forms, one the R-configuration, the other the S-configuration. Be sure you know which one is which.

Remember: conformations can be changed by rotating bonds; configurations can be changed only by breaking and reforming bonds!

Extending the carbon chain --- propane and butane

In replacing one of the hydrogens of ethane with an additional carbon and its associated hydrogens, as was previously found in the extension of methane, all hydrogens are equivalent, and only one propane (C3H8) can result. Consider just a few of the possible representations that might be used to describe this simple hydrocarbon:


In further extending the carbon chain of propane, the choice of hydrogen for replacement by carbon is not as simple as it was for the methane or ethane extension. For propane, all hydrogens within the molecule are NOT identical. There are in fact TWO different types of hydrogen available for replacement --- six of one type (2 equivalent CH3's) and two of a second type (a single CH2 in the middle of the molecule). That's a consequence of there being two types of carbon in the propane to start with. The two outer carbons are each bonded to ONE other carbon in the molecule. Any carbon bonded to only one other carbon is called a PRIMARY CARBON; all hydrogens bonded to a primary carbon are called PRIMARY HYDROGEN's. The inner carbon of propane is bonded to TWO other carbons in the molecule. Any carbon bonded to only two other carbons is called a SECONDARY CARBON; all hydrogens bonded to secondary carbons are called SECONDARY HYDROGEN's.

The hydrogen for replacement therefore can be either a primary hydrogen, yielding a linear form of the C4H8 hydrocarbon, or a secondary hydrogen, yielding a branched form of the same molecule.



Notice that in the branched structure, an additional type of hydrogen can be identified. The central carbon of this molecule is bonded to THREE other carbons; any carbon bonded to three other carbons is called a TERTIARY CARBON; any hydrogen bonded to a tertiary carbon is called a TERTIARY HYDROGEN.

In providing suitable names for these two structural isomers, we first encounter the ambiguities and confusion associated with the use of multiple nomenclatures that have evolved over the years. In using "common" names, the linear form of butane would be called n-butane, where the "n" signifies normal, or non-branched, while the branched form would be called iso-butane, where the "iso" prefix denotes isomeric. According to the more systematic IUPAC (International Union for Pure and Applied Chemistry) rules, the linear form is called simply butane (linearity is assumed) and the branched form is called methylpropane. No positioning number for the methyl group is required, because in any other position, the structure would actually be the linear butane.

Proceed to the Self Test for Module #1.

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