Organic

Organic chemistry involves the study of the chemistry of carbon-containing compounds (organic compounds). At first glance, one may think this to be a relatively small area of chemistry. In fact, Carbon-containing compounds comprise over 90% of all known compounds. This could be due in part to the fact that there are many areas of research in organic chemistry and thus, many compounds have been discovered. It is, however, largely due to the vast number of compounds that carbon and hydrogen (and a few other elements) form.

Organic compounds contain mostly hydrogen and carbon. Those compounds containing only these two elements are called hydrocarbons. Hydrocarbons can have single-, double-, and triple- CC bonds, they can form many branches and ring structures and form a large part of chemistry. More interesting in their reactivity, however are compounds that contain atoms other than these two. We call these other atoms heteroatoms to refer to the fact that they are other than hydrogen and carbon. Heteroatoms cause changes in the reactivity (or function) of the organic compound and the locations in the molecules where these groups exist are called functional groups. For example, a very common functional group that contains a single oxygen-hydrogen pair is the alcohol group. for example, methanol is CH₃OH and ethanol is CH₃CH₂OH. Other functional groups include carboxylic acids -COOH, ethers Amines -NH₃, etc. These actually make up the compounds of most interest to organic chemists.

Alkanes

The simplest class of organic compounds (but not limited to simple molecules) is called alkanes. An alkane is a compound made up of only hydrogen and carbon (hydrocarbon) that has only single bonds in it. Of these, the straight-chain hydrocarbons are the easiest to deal with. These compounds are called straight-chain not because the line of carbons forms a straight line but because they form a continuous line. The following table lists a few straight-chain hydrocarbons and gives names and properties

The general formula for alkanes is C_nH_2n+2. It is interesting to note that as the alkanes get larger, their boiling and melting points get higher. This makes sense on two counts: the heavier the molecule, a) the more energy it needs to be "lifted" out of the liquid phase, etc. and b) the larger chains get tangled in each other, making the un-tangling process nearly impossible.

Structural isomers

Alkanes can form many compounds, often, several compounds with the same chemical formula can have different structures. Compounds with this relationship are called structural isomers of each other.

Note that Petrucci uses the term "positional isomers" to represent that the branches are attached at different positions. "Positional isomers" are not distinct from "structural isomers", merely a specific sub-group of structural isomers

For example, consider a hydrocarbon with four carbons, C₄H₁₀. This molecule can be represented as a straight-chain

(common name: isobutane, IUPAC name: 2-methylpropane or just methylpropane; the 2 is redundant since there is no other place for a branch to go.)

These molecules both have the same chemical formula but are obviously different in their connectivity (structure). They are structural isomers of each other.

These three molecules are all structural isomers of each other, i.e., they all have the formula C₅H₁₂ but they have different connectivities (structures).

Remember, these structural formulas are not real three-dimensional representations of the shape of the molecules themselves. They merely map out the way the atoms are connected. No information is implied regarding the orientation of these molecules based solely on structural drawings like these, except in special cases which we'll get to later.

Thus, for example, the molecule methylbutane can equally well be represented as any one of the following structures (hydrogens not shown for simplicity).

Conformers

In the previous discussion of structural isomers, we stated that the 3-D representation of the molecules was nearly completely neglected in the structural drawings we normally create to represent the various molecules. If we study for a moment the 3-D arrangement of atoms in a simple molecule, we see that this adds to the level of complexity that we need consider to completely understand a given molecule.

In the case of alkanes (no double bonds or ring structures) there is (in principle) free rotation around any of the single bonds in the structure (as around single bonds in any chemical structure). Thus, it is not correct to write down a single picture of the molecule and expect that that is how it always looks. If we consider the two-carbon alkane ethane we see that the Methyl groups can rotate around each other such that at one instant, the hydrogens of one methyl group are exactly aligned with those of the other group. This arrangement is called the eclipsed conformation since the hydrogens eclipse each other when viewed down the axis of the molecule. On the other hand, a slight rotation of one methyl group compared to another brings the hydrogens out of alignment to a conformation called staggered. In this case, all six hydrogens are visible when viewed down the molecular axis. Study the drawings and manipulate the 3D models below to satisfy yourself that you understand this.

These two images show us instantaneous pictures of the geometry of this molecule, in reality, it is rotating so fast about the C-C bond that the two orientations swap more than 10⁶ times per second. Some molecules with bulkier groups instead of hydrogens can find themselves trapped in one conformation or another. This can lead to observed differences in the properties of the two conformers (isomerism), as if they were in fact isomers.

In order for molecules to reach their lowest possible potential energy, the individual atoms must all be free to find the best positions that optimizes the overlap of orbitals. if there are near-neighbor atoms that interfere with this freedom of motion, there can be strain on the bonds such that the molecule has a less than optimal potential energy (higher PE). In the two molecule conformations above, the eclipsed conformation would be higher in PE than the staggered because the steric interaction of the two hydrogens is greater when they are eclipsed than when they are staggered, i.e., they bump into each other more. If there were other groups like methyl or ethyl groups then we would see even more steric interaction and hence, even higher PE as these groups interact more.

In these later cases, we call these different conformations "conformational isomers", since there would be a whole series of differing potential energies, depending on eclipsed versus staggered and also depending on which groups are next to each other.

Cycloalkanes

A further step in the complications of structures of alkanes involve the possibility that a ring structure may be formed. If no C=C double bonds exist these compounds are called cycloalkanes. They have the general formula (CH₂)_n. Let us consider just the first few cycloalkanes.

C₃H₆: cyclopropane

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This molecule has bond angles of 60º even though the carbons are all SP³ hybridized. Thus, the atomic orbitals cannot overlap as well as they would if the molecule were unconstrained. We would thus expect that the energy of such a bond is higher than that of a normal C-C single bond not constrained by geometry. This is experienced in the exothermic reaction whereby the ring is opened with the addition of two hydrogen atoms.

C₄H₈: cyclobutane click for 3d view

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This molecule, like cyclopropane is strained since the bond angles must be, on average, only 90º as compared to the tetrahedral angle of 109.5º. Thus, the C-C bond in cyclopropane is also higher in energy than the C-C bond in a non-constrained alkane. Actually, for other reasons, this molecule is not exactly flat. One of the carbons is raised out of the plane of the molecule a few degrees.

C₅H₁₀: cyclopentane click for 3d view

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The bond angle in this molecule is on average 108º, very close to the ideal tetrahedral angle. There is little strain on the bonds here. Cyclopentane is a relatively stable molecule. Due to steric interactions of hydrogens with other hydrogens, this molecule is actually slightly puckered. See the three-dimensional model to visualize this.

All the above molecules are nearly flat molecules on the time average at room temperature (not counting the hydrogens). Actually, cyclopentane is slightly puckered at absolute zero, as shown (exaggerated) in the 3d model. No other cycloalkanes are flat. Let's look at the next in the series to see why.

The "flat" molecule would have a bond angle larger than the tetrahedral angle. This angle could easily be reduced to the tetrahedral by merely bending the molecule out of its flat configuration. The two possible conformers of the non-flat cyclohexane are the chair and the boat as indicated in the drawing below.

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In these conformations, the carbon atoms can assume more closely the ideal tetrahedral geometry of the sp³- hybridized atoms they are.

Naming (Nomenclature)

It is obvious that using the chemical formula alone is not sufficient to uniquely identify the vast majority of organic compounds. Structural formulas too are difficult to use and impractical to put in spoken language. Originally, names for compounds were not well coordinated and there were often compounds that had been named by different people completely different things. It was very hard to determine exactly what chemical the names were referring to without first researching the history of each individual name. A structured naming regime called IUPAC is now in place to help us both name new compounds and rebuild the structure of named compounds. This set of rules helps us to uniquely identify each chemical compound by its name alone. One drawback to this scheme is that the names can become quite long. For a more complete listing of the IUPAC rules than I can give in these lecture notes, click here,

Let's look at the some of the rules to help you learn how to use this nomenclature scheme.

1. Parent Chain

Select the longest continuous 'chain'. It is the parent chain. It's name is used as the last part of the compounds name. If there are several "longest" chains within the molecule of the same length then the parent chain will have the most possible branches and will have the lowest possible branch numbers of all the choices. Take, for example, the molecule pictured below (C₆H₁₄).

The longest straight chain is a four carbon chain (Numbered in blue). There are several possible choices for the four-carbon chain. It makes no difference which you pick. I chose the four carbons (blue numbered). Avoid the erroneous thinking that the 'chain' must be linear along the paper. This is not the case. Check out the 3D model and prove this for yourself.

2) Numbers

Number the carbons in the parent chain (and in the branches) such that the branches (and any other non-alkane features like double bonds, hetero-atoms, etc) occur at the lowest possible number carbon. Start with the first branch, if there are two ways to number the parent such that the first branch occurs on the same number then chose the one which gives the smallest numbered second branch, etc. In the above example, the numbering sequence could have been reversed with no difference in the location of the branches.

3) Branches

The branch names are those of the normal alkane of the same length but with the -ane suffix replaced by -yl (indicating a molecular fragment) thus, methane becomes methyl for a one-carbon chain, etc.

You now prefix the parent name with the chain names, indicating their location on the parent chain. In the above example, there are two methyl chains, located at carbons 2 and 3 on the parent chain. Hence, we use the prefix 2,3-dimethyl to describe the location and type of branches on the parent.

In this example, the completed name is 2,3-dimethylbutane. NOTE: no spaces in the name.

4) Double bonds and triple bonds

Double bonds and triple bonds are indicated by changing the ane to ene and yne, respectively, in the name of the chain. They should be included as part of the parent chain, even if a longer chain is possible but which excludes this functional group. The location of the functional group (double or triple bond) is indicated as the first carbon in the chain that has that type of bond.

CH₃-CH=CH-CH₃ 2-butene (Note that there are cis and trans isomers of 2-butene. See Geometric Isomers below)

5) Cycloalkanes

Cyclic alkanes should be the parent chain in a compound (unless there is a "straight-chain" part that is larger or which contains an important functional group). If more than one cycle, then the largest one is the parent. Prefix the normal alkane name with "cyclo-" to make the name. Thus, a three-carbon ring is cyclopropane (see above) and a four-carbon ring is cyclobutane (see above). If there are substituents or branches on the ring, then numbering of the carbons is done such that they occur at the lowest possible numbered carbons. See the drawing below as example.

(Note: always put the substituents in alphabetical order and name it so. Also note that there is an alternate naming scheme where the largest substituents is first. I prefer the former method)

In the case where the acyclic part is longer than the cyclo part then the cyclo part is named as a cycloalkyl branch.

In this case, the cycloalkyl is called 3-methylcyclohexyl and it's on carbon 1 of a heptane parent chain. Thus the name is 1-3-methylcyclohexylheptane.

6) Arenes

Arenes are a special class of organic compounds. They have what is called a conjugated p-bond system that rapidly resonates, creating a large delocalized orbital. This large delocalization creates an especially stable molecule towards certain types of reactions. The most common arene is a six-member ring of carbons where each carbon has one hydrogen on it, called benzene.

The alternating double and single bonds seen in the two resonance structures to the left of the double arrow

helps us to see the number of bonds but don't properly indicate that all carbon-carbon bonds are in fact equal in all respects. The overall resonance can be represented by the right-hand diagram where the double/single bonds are replaced by the circle indicating that the ring is aromatic. This, however is not a "Lewis Structure" in the classical sense since you cannot tell how many bonds each carbon has.

Substituent groups can exist on these rings, numbering is such that they occur at the lowest possible numbers. Let's look at some specific examples:


1,2-dimethylbenzene (orthodimethylbenzene)	1,3-dimethylbenzene (metadimethylbenzene)	1,4-dimethylbenzene (paradimethylbenzene)

Note that there is an alternate form of naming the location of the substituents on a benzene ring. This is not strictly IUPAC but is very commonly used. The prefix ortho indicates the adjacent position, meta indicates two positions away and para indicates directly across from (3 positions away).

	naphthalene
	anthracene
	pentacene (blue)
	coronene (yellow)
	graphite (black)

Here are a few examples, Name the following: (click on the drawing for the name)

Now, draw the structures corresponding to the following names (click on the names to see the answer).

Branched Alkyls.

As we have seen above, it is possible to get branches on the branches of our alkanes. These branched alkyls must also be named using the same rules we've seen above for the main-chain alkanes.

There are a few common names that are often used as a part of a "IUPAC" name. If you recall the molecule isobutane (see above) which consisted of a three-carbon chain with a methyl group on the 2 position. It is more correctly named 2-methylpropane or just methylpropane (the 2- is redundant). There are many molecules that contain a group that could be classified as a three-carbon chain attached at position 2 rather than position 1. Take for example, the following two molecules.

Molecule 1 has a three carbon branch joined at the end to carbon 4 of the main chain. Since a three carbon chain has the root "prop" and this chain is a branch (suffix of yl) it is a propyl group. although it serves no purpose this time, the carbons on this group are numbered as shown, starting with the propyl carbon that's bonded to the main chain.

4-propylheptane

IUPAC: 4-1-methylethylheptane

or use the shortcut
(also allowed by IUPAC)

4-isopropylheptane
(isopropyl group is shown here in red)

We can also look at the name of the three-carbon group in molecule 2. In this case, the propyl group is not attached at the end. It's attached in the middle. We must start numbering from the carbon attached to the main chain, thus, we find a two-carbon chain with a methyl branch on carbon 1. Hence the IUPAC name is 4-1-methylethylheptane. In this case, we can use the shortcut prefix "iso" to give this branch a simpler name. Rather than a 1-methylethyl group, we can call it an isopropyl group and thus the name of the molecule is shortened to 4-isopropylheptane.

If we have a 4-carbon alkyl group, rather than the three carbon one above, there are more possibilities.

Recall that there are 2 structural isomers of the 4-carbon alkane. These two can each attach to a larger main chain in two ways. They can use a terminal carbon or a middle carbon. Thus we can find 4 different 4-carbon alkyl groups are possible. In the following molecules, I will not draw the main chain. I will represent it merely as R (the Rest of the molecule)

* In a couple of cases, we have some prefixes we've never seen before. Prefixes sec- and tert- (or sometimes t-) refer to secondary and tertiary, respectively. These terms refer specifically to the number of carbons in the branch attached directly to the root (carbon 1)

A carbon is considered a primary carbon if it has only 1 other carbon attached to it on the branch In this case, the carbon is at the end of a chain. For example the ethyl group

can only have a primary carbon (in red). The propyl group could have a primary

or a secondary

carbon, depending on where the R is attached. In the case of the secondary carbon (in the branch called 1-methylethyl), there are 2 other carbons bonded to that carbon. (we don't use the name sec-butyl for this alkyl group since a more common shortcut is isobutyl as is indicated above.

The butyl group can have a primary,

, a secondary,

, or a tertiary carbon,

, depending on the structure. The tertiary carbon is one with three other carbons attached.

Geometric isomers.

There are times when molecules can have the same formula and the same structure (same connectivity) but are not the same molecules. The difference lies in how the substituents occupy the space in the molecule. These are classed into a general category called Stereo Isomers. Of these, Geometric Isomers forms a sub group.

Actually, this example is more complex than it seems. The molecule, at first glance seems simpler than example b a few pages back. This is not the case. Because there is no free rotation about the double (or triple) bonds it is possible to have different isomers where the structure of the isomers is identical but where the geometric arrangement is not the same. Thus, we create geometric isomers. This is different from the conformers that we saw earlier where free rotation easily (some times) converts one geometric arrangement into another. Here, the geometric arrangements are not changeable without breaking a bond.

We can see two distinct isomers because the position of the CH₃ group relative to the ethylene group on the other side of the (right=hand) double bond is different from one case to another. In one case, the non-hydrogen constituents are on opposite sides of the double bond. This is the trans configuration. In the other case, the non-hydrogen constituents are on the same side of the double bond. This is the cis configuration. thus, the names for these two molecules are trans-2-methyl-2,4-hexadiene and cis-2-methyl-2,4-hexadiene, respectively. Of course, there are always more complex cases were these simple rules break down and need refinement. We can't cover all the rules in just a few hours worth of lectures.

Note that although there were two double bonds in these isomers, only one of them (highlighted) contributed to cis/trans isomerization. The other double bond in each group (not highlighted) have identical groups on one end (methyls) and thus, there can be no cis/trans isomers formed about that bond.

It is also possible to get cis-trans isomers from other molecular structures where rotation about a bond is not possible, for example, in cyclo- compounds, the ring prevents free rotation as follows.

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cis-1,2-dimethylcyclopentane	trans-1,2-dimethylcyclopentane

NOTE: The two drawings on the right are both the same structure and geometry and therefore with the same name. However, they are not quite identical. They are in fact optical isomers (enantiomers) of each other. Chemically, they are identical (except to enantiomeric reactants and catalysts like enzymes) but optically they are different. Optical isomers can only form if there is 3-d structure in the mode (for example tetrahedral carbons). If the molecule has planar symmetry (trigonal planar carbons) then any mirror image is also super imposable. A simpler set of enantiomers can be found in the VSEPR chapter where I discussed a tetrahedral carbon with 4 different substituents on it.

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These molecules are optically active (they plane-rotate polarized light). The pair are enantiomers (optical isomers) of each other. Individually, any molecule that displays optical activity is called chiral and the amount and direction of it's optical activity is termed it's chirality.

Functional groups

Functional groups (other than double and triple bonds) occur whenever a heteroatom (not carbon or hydrogen) is incorporated into the structure. The following is a quick list of functional groups and some quick information on naming them.

Alcohols

Alcohols are identified by presence of an OH group on a hydrocarbon chain (R-OH). These compounds are usually named by appending -ol to the end of the name and sometimes, indicating the location of the functional group using numbers as previously described. Below are a few examples of alcohols and their names.

There are several types of alcohols, ethanol and methanol have their functional group on a terminal carbon and are called primary alcohols (the carbon to which the OH is attached has at most one other carbon attached to it. R-COH.

Secondary alcohols occur when the functional group occurs in the middle of the chain, as in 2-butanol. Here, the alcoholic carbon has two other carbons bonded to it, hence the terminology secondary.

2-propanol could also be named accordingly as sec-propanol. (sec means secondary).

Tertiary alcohols involve alcoholic carbons with three other carbons bonded to them. In this case, the OH occurs just at the junction between two alkane chains as in:

There are also diols and triols (and more), where more than one OH group exists on a single carbon chain.

Ethers

An ether group contains two hydrocarbon chains connect by an oxygen atom (R-O-R'). Simple ethers can be names by simply naming the two branches first and then prepending them to the word ether. Alternatively, more complex molecules can be named by considering the R-O group to be the alkoxy group and simply treating it like a branch on the larger molecule. Below are a few examples, some use both naming conventions. Numbering if necessary is done in the normal fashion.

Aldehydes

such compounds are named by adding the suffix -al. Numbering is not necessary since the functional group must be (by definition) at the end of the carbon chain, therefore, it is always attached to carbon #1.

Notice that these molecules are all drawn with the aldehyde carbon looking to have bond angles of about 120º. That's because the C=O unit means the carbon is SP² hybridized and is therefore trigonal planer with bond angles of approximately 120º. It's best to represent the true geometry of at least the planar portions of molecules when you can and we do here.

Ketones

Here, the R chains may or may not be identical, hence the prime on one of them. Here, however, we treat the entire chain (R-C-R') as a single unit when naming and simply indicate the carbon number where the double bonded oxygen occurs (if necessary).

Carboxylic acid

In this functional group, we combine the OH and the C=O on one carbon and the new functional group is a carboxylic acid( wpe11.jpg (1326 bytes)

). This group is obviously always located on the terminal carbon of a hydrocarbon chain. It is named using the name of the hydrocarbon parent chain and the suffix -oic acid. Below, find some examples, alternative common names are give in parenthases.

Esters

When naming an ester, we use the names of the component alcohol and of the carboxylic acid and append the suffix -oate.

Amines

Amines are compounds containing nitrogen, cf., ammonia (NH₃). There are three types of amines.

Primary amines have only 1 carbon attached to the nitrogen. Secondary amines have two carbons attached to the nitrogen and tertiary amines have three carbons attached to the one nitrogen atom.

We name the amines by simply naming each of the R groups alphabetically as we do branched on an alkane and ending the name in amine.

In some cases, the groups attached to the nitrogen are more important (or complex) that the amine and naming is simplified by treating the amine as the branch rather than the parent. In this case, we name the amine and append the letter o to the end and then name the parent.

Other amines simply use the common name since other conventions become too complicated.

Amides

These are the compounds that hold your DNA and RNA in their double helix shape. An amide is like a carboxylic acid but where the OH group is replaced by an amine group, for example, NH₂ or NHR or NRR'.

These molecules are easier to name. Simply name the carbon chain and then add the suffix amide.

Reactions

Reactions of Alkanes

Burn in air to give carbon dioxide and water. This is the ultimate in a series of oxidation reactions of hydrocarbons. Lesser oxidation reactions would form alcohols, aldehydes, keytones and acids. We won't delve into those in this course.

Cracking (in oil refining, used to reduce the molar mass of the compounds so they can be used as gasoline, etc.) Cracking Explained Details

Reactions of alkenes and alkynes

Addition reactions

This is an alkylide ion (in this case, the ethylide ion ) and as a group, they are excellent nucleophiles for use in building up molecules via the substitution reaction (see SN1 and SN2)

Elimination Reaction (opposite of addition)

A saturated hydrocarbon (as many hydrogens as possible) is converted to an unsaturated hydrocarbon by 'eliminating' a hydrogen molecule. This is also called dehydrogenation.

Substitution Reactions

In a substitution reaction one substituent is substituted for another. A very common type of substitution involves the replacement of a leaving group X ( X is something that can leave the molecule relatively easily, such as a halide) by a nucleophile Nu (~phile implies "attraction to" so a nucleophile is attracted to the positive charge of a nucleus). I will use Nu to stand for the generic nucleophile. Normally, a nucleophile is negatively charged or polar with lone pairs of electrons. These can be used to form new a new bond with the nucleus (carbon atom) involved. There are two types of Nucleophilic Substitution, S_N1 and S_n2:

S_N1

In an S_N1 process, there are two steps involved. The first step (the slow step) involves only the starting molecule, the nucleophile is not involved. Hence the 1 of S_N1 means 1 molecule is involved (unimolecular). In this step, the leaving group takes its pair of electrons and leaves behind a positively charged trigonal-planar carbon (alias carbocation). Then the nucleophile bonds to the carbocation. In this case, because the intermediate is symmetrical, before the nucleophilic attack, there are two possibly products, depending on the side from which the nucleophile attacks.

In this reaction mechanism, because the nucleophile is just as likely to attack from the left as from the right, we will get a 50:50 mixture of the two products. If the reactant was chiral (optically active) then the two products are both chiral but of opposite chirality. The mixture will display no optical activity since the two products optical activities cancel each other out. This is a racemic mixture.

S_N2

In the S_N2 process, the nucleophile bonds to the carbon while the leaving group breaks its bond in a concerted step. This first step (slow) involves 2 molecules simultaneously (bimolecular), the starting material and the nucleophile, hence the 2 in S_N2. At the intermediate (or transition state), the positions of constituents ABC move to a planar orientation with the Nu on one side and the leaving group X on the other to form a trigonal bipyramidal intermediate (transition state). As the nucleophile moves closer with it's lone pair, the leaving group departs, taking its bonding pair as a lone pair and taking the excess charge in the process. The spatial orientation of the groups ABC is reversed in the process. In the case of an optical isomer (chiral molecule) the chirality (direction that light is rotated) is reversed.

Note that in the case of S_N2 reactions, the carbon is tetrahedral when the Nucleophilic attack occurs. This means that there is greater possibility of steric hindrance. If the carbon on which the reaction should occur is tertiary then an S_N2 reaction is unlikely and an alternate reaction processes may then dominate.

Readings for this section

Organic Chemistry 2007-03-26

Naming (Nomenclature)

1. Parent Chain

2) Numbers

3) Branches

4) Double bonds and triple bonds

5) Cycloalkanes

6) Arenes

Alcohols

Ethers

Aldehydes

Ketones

Carboxylic acid

Esters

Amines

Amides

Reactions of Alkanes

Reactions of alkenes and alkynes

Addition reactions

Elimination Reaction (opposite of addition)

Substitution Reactions

SN1

SN2

Prof. Michael J. Mombourquette. Copyright © 1997 Revised: March 26, 2007.

S_N1

S_N2

Prof. Michael J. Mombourquette.
Copyright © 1997
Revised: March 26, 2007.