STRUCTURES AND NOMENCLATURE - ORGANIC CHEMISTRY - The Handy Chemistry Answer Book (2014)

The Handy Chemistry Answer Book (2014)

ORGANIC CHEMISTRY

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STRUCTURES AND NOMENCLATURE

What is an organic compound?

Any molecule, or compound, that contains carbon atoms is referred to as “organic.” The usage of this term is a bit arbitrary, though, as some forms of carbon (like graphite and diamond) and carbon-containing ions (like formate and carbonate) are not thought of by chemists as “organic molecules.”

Where do I run into organic chemicals in my life?

The food you eat, the clothes you wear, the gasoline in your car, the plastic bags you may (or may not!) get at the grocery store…. The list could go on forever.

Why have chemists devoted so much focus to the chemistry of carbon?

Because it’s everywhere! Carbon is the fourth most abundant element in the universe (fifteenth on our planet), and the building blocks of life (DNA, amino acids) all contain many carbon atoms. Many biologically active molecules and medicines rely on carbon to define their overall shape.

What was the first organic chemical ever synthesized in a lab?

Urea. In 1828 Friedrich Wöhler was trying to make ammonium cyanate (NH4+CNO), but this salt turned out to be unstable. It reacted to form urea, demonstrating for the first time (arguable according to some) that an organic chemical could be made from inorganic starting materials.

What else did Friedrich Wöhler discover that helped make him famous?

Not only is Wöhler known for making the first organic chemical outside of a living cell, he also discovered the elements beryllium (independently discovered by Antoine Bussy), silicon, aluminum, yttrium, and titanium. In case that wasn’t enough to cement his position in the annals of chemistry, he also discovered that meteorites contained organic compounds and developed a process to purify nickel.

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How many bonds can carbon form?

Carbon has four electrons available for bonding with other atoms. When carbon is bonded to four other atoms, they are arranged in a tetrahedral geometry. These two simple bonding rules have important consequences, as we’ll see in this chapter.

What types of bonds can carbon form?

Carbon can form single (σ) or double (π) bonds to other elements. Double bonds use two of carbon’s four available electrons, so carbon can form two double bonds (like carbon dioxide, CO2), or one double bond and two single bonds (like formaldehyde, H2CO), or four single bonds (like methane, CH4).

Can carbon form more than one π-bond?

Yes, if two carbon atoms form one σ and two π bonds (for a total of three bonds, known as a triple bond), the group is called an alkyne. The simplest alkyne is acetylene (C2H2). Welding torches use a combination of oxygen and acetylene to reach temperatures of over 6000 °F (3300 °C).

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What is the shape of a carbon-carbon double bond?

The geometry of the carbon atoms in double bonds is planar. This shape comes from the hybridization of the carbon atom, which is sp2 (one p orbital is not involved in forming single bonds). To get a bonding interaction between these two remaining p-orbitals, they have to overlap in space. So in a molecule like ethylene (C2H4), all of the hydrogen atoms are located in the same plane.

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What are hydrocarbons, and how many different ones are there?

Hydrocarbons, as you might have figured out from the name, are molecules that contain only hydrogen and carbon atoms. There are literally an infinite number of ways to arrange these two elements together, especially if you include polymers (see “Polymer Chemistry”). Hydrocarbons are important molecules. Different sizes and types of hydrocarbons are known as natural gas, gasoline, waxes (like candles), and plastics.

How do chemists name so many different hydrocarbons?

With a bunch of rules! Let’s start with just straight chains of carbon atoms. Here we just need to define how many carbon atoms there are in the molecule. If the molecule doesn’t have any double bonds, we use the suffix “-ane.” The prefix indicates how many carbon atoms there are. Most of these prefixes are based on Greek numbers (one is Latin, and a few are just weird). Collectively, these molecules are called alkanes.

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Are hydrocarbons always straight chains of carbon atoms?

No. There could be carbon atoms attached to the linear chains we talked about in the previous question. Let’s learn the next step in naming alkanes and have a look.

First, we need to define the names of branches (see graphic, next page). Chemists use the same prefixes to indicate the length of the branch, but now the suffix is “-yl” instead of “-ane.” So methane (CH4), when it’s a branch off of a chain of carbon atoms, becomes methyl (-CH3), ethane (CH3CH3) becomes ethyl (-CH2CH3), and so on.

Next we have to indicate where along the main carbon chain the branch point is. This part is pretty simple—just number the carbon atoms and put this number before the name of the branch. So if you had an eight-carbon chain (octane) with a two-carbon branch (ethyloctane) on the third carbon from the end, it would be called 3-ethyloctane and look like this:

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Hydrocarbons with additional atoms attached to linear chains have suffixes ending in “-yl” instead of “-ane.” Here are some examples.

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There are a lot more rules to naming organic compounds, but that’s enough for now.

Can carbon chains form rings, too?

Yes—chains of carbon atoms can connect back to themselves, forming rings of atoms. The prefix cyclo- is added to the name of the linear carbon chain to indicate that a ring is present (so hexane becomes cyclohexane). The chemistry ring structures can be different than their linear cousins because of the added energy that some rings contain. We know that sp3-hybridized atoms like to form bonds that are separated by 109.5°. The more that a ring forces those bonds to deviate from that ideal angle, the more energy (called ring strain) that is released when that ring is opened during a chemical reaction.

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What is the structure of diamond?

Diamond has a repeating structure of carbon atoms in which all the atoms are bonded to four others in a tetrahedral geometry. It’s easiest to see if we first look at the structure of cyclohexane, a ring (cyclo-) of six carbon atoms (-hex-), with no double bonds (-ane).

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If we repeat the structure of cyclohexane over and over, we arrive at the structure for diamond.

What is charcoal?

Charcoal is made of carbon and ash and is formed when water and other substances are removed from animals or plants. It can be produced by heating wood or other biologically derived materials in the absence of oxygen.

What is a heteroatom?

A heteroatom is any atom that is not a carbon or hydrogen atom. Some examples of typical heteroatoms include oxygen, sulfur, nitrogen, phosphorus, chlorine, bromine, and iodine, though anything other than carbon or hydrogen fits the definition.

What is a chalcogen?

A chalcogen is an element in group 16 on the periodic table. This includes oxygen, sulfur, selenium, tellurium, polonium, and livermorium. This name comes from the Greek word meaning “copper-former,” and has its origins in the fact that some of these elements tend to coordinate to metals to form compounds with metals in ores.

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The structure of a diamond crystal.

What is a cation?

A cation is a positively charged atom or molecule. Cations have a larger number of protons than electrons, such that they have a net positive charge.

What is an anion?

An anion is a negatively charged atom or molecule. Anions have a larger number of electrons than protons such that they have a net negative charge.

What is a free radical?

A free radical is an atom or molecule that contains unpaired electrons in one (or more) of its orbitals. Typically these species will be highly reactive as the unpaired electron(s) can pair with other electrons in a favorable manner. Radical species can have any charge or be neutral.

What are isomers?

Isomers are chemical compounds with the same molecular formula, but which are different in some way. The major types are constitutional isomers, stereoisomers, and enantiomers (the last one is actually a subset of the second-to-last one, but we’ll get there in a minute).

Constitutional, or structural, isomers have the same number of atoms, but they are arranged in a different order. For example, four carbon atoms and ten hydrogen atoms can be arranged in two different ways.

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What is a geometric isomer?

Geometric isomers are molecules containing the same set of atoms and bonding arrangements, but with a different spatial arrangement of the atoms or groups. For example, cis and trans isomers are an example of geometric isomers.

What are stereoisomers?

Stereoisomers have the same number of atoms connected in the same order, but differ in their arrangement in space. There are two major types of stereoisomers: enantiomers and diastereomers.

What is chirality?

Chiral objects have nonsuperimposable mirror images. What does that mean? Superimposable means one object can be placed over another, or less technically, that they’re identical. So enantiomers are not identical, but they are mirror images. Take a look at your hands—they are enantiomers. If you put one hand up to a mirror, it looks like your other hand (so they are mirror images). But if you try to put one hand on top of your other (no, not palm to palm, that’s cheating), you see they’re not identical (therefore nonsuperimposable).

What are enantiomers?

Enantiomers are molecules that are chiral. In organic chemistry, if a carbon atom is bonded to four different atoms (or groups of elements), then we can draw two enantiomers of the molecule. Remember that the connectivity does not change, just the arrangement of the atoms in space.

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Wait—what do those dashed and wedged bonds mean?

Up to this point we’ve mostly been representing molecules as flat objects, where chemical bonds are just shown as straight lines. But molecules are not flat. In the previous question, the four halogen atoms around the central carbon form a tetrahedron. Chemists use dashed bonds to indicate that they are behind the plane of the paper, and wedged bonds come toward you, above the plane of the paper.

What are diastereomers?

This is going to sound like a cop-out, but diastereomers are stereoisomers that are not enantiomers. That’s the real, technical definition. One type of diastereomers show up when carbon forms a double bond. Recall from previous chapters that when there are three groups bonded to a carbon atom, it will be planar (sp2 hybridized). If the double bond is in the middle of a carbon chain, there are two possible isomers.

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These two molecules are not superimposable, but they’re also not mirror images, so they are called diastereomers. There are many other forms of diastereoisomers, but this form is the easiest to understand.

What is a racemic mixture?

A racemic mixture contains equal amounts of both enantiomers of a molecule.

What does enantiomeric excess measure?

The enantiomeric excess is a measure of how much more of one enantiomer is present in a mixture. It’s often reported as a percentage. Racemic mixtures have an enantiomeric excess value of 0% because both enantiomers are present in equal amounts. For a solution composed of 75% of one enantiomer, the enantiomeric excess would be 50% (75% – 25% = 50%).

How and when was molecular chirality discovered?

Nonracemic mixtures rotate the plane of a beam of polarized light in either a clockwise or counterclockwise direction. Jean-Baptiste Biot, a French physicist, observed this effect in 1815 with quartz crystals, turpentine, and sugar solutions. These were important results in understanding the nature of light, but it was Louis Pasteur in 1848 that figured out that the effect was based on molecular properties. Pasteur painstakingly separated enantiomerically pure crystals from a racemic mixture of tartaric acid and showed that the two enantiomers rotated light in opposite directions.

Are all the carbon-carbon bonds in benzene the same length?

Yes, but you might not think so by looking at a single line structure of benzene. The actual structure of benzene is a combination of two structures, shown below. In technical terms, the electrons in the p bonds are delocalized (spread out) by resonance. The drawing convention that chemists use to represent molecular structure just can’t display this properly in a single structure. The electrons do not move from one place to another, and the carbon-carbon bonds do not oscillate between long and short—the structure is an average of these two drawings. After all, a molecule of benzene doesn’t really care that we can’t properly draw it.

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Sometimes, you might see benzene drawn with a single circle in the center, representing the delocalization of the π-electrons.

What is resonance?

Resonance is a way that chemists represent delocalized electronic structure. Let’s take that statement apart to understand what it means. “Delocalized” means that an electron, or a pair of electrons, is not located entirely around a single atom or bond. Take a look at the two structures of nitrogen dioxide (NO2) on the following page. The negative charge is located on one oxygen atom in one resonance structure, but can be found on the other oxygen in the second resonance structure. Notice that we said “electronic structure” and haven’t said anything about atoms moving here—that’s because they don’t. Resonance only deals with electrons, and the atoms are located in the same arrangement in every resonance contributor. This is important, and makes sense if you remember that the electrons aren’t “moving” from one resonance structure to another. These structures are needed because the actual molecule is more complicated than our simple drawing system can represent.

When was the term “aromatic” first seen?

It was first seen in a chemistry publication in 1855. The paper was written by August Wilhelm von Hofmann, but he gives no indication why he chose this term. It’s an unusual case since only a few aromatic compounds are actually smelly, while many nonaromatic compounds in chemistry labs do truly stink.

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What is aromaticity?

Aromaticity is a special kind of resonance delocalization, one we’ve actually already seen. Delocalization of electrons always makes molecules more stable (compared to imaginary molecules where the electrons cannot spread out). If this delocalization takes place in a flat ring of n carbons, and the number of electrons involved is 4n + 2 (i.e., 2, 6, 10, 14, etc.), then the system is called aromatic.

What is a functional group in organic chemistry?

Functional groups are groups of atoms that tend to show similar reactivity in different molecules. Chemists use these groupings to help understand and predict how different molecules react with each other, and they’re also used for naming compounds.

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Some examples of functional groups.

What is a carbocation and what is a carbanion?

A carbocation is a positively charged compound in which a carbon atom takes on a significant fraction of the positive charge. The definition for a carbanion is probably easy to guess, then—it’s a negatively charged compound in which a carbon atom bears a significant fraction of the negative charge.