Structure and Bonding

Hydrocarbons Organic chemistry is the study of the compounds of carbon, principally the hydrocarbons and their derivatives. A hydrocarbon is a compound that contains only carbon and hydrogen. Carbon and hydrogen can unite to make compounds that contain long chains of carbon atoms, rings, and multiple bonds between two carbon atoms. The following graphic shows models of hydrocarbons. These compounds contain only C and H atoms.

Note: Every C has four bonds (lines) and every H only one.

The number of hydrocarbons is enormous and justifies a branch of chemistry called organic chemistry. Derivatives of hydrocarbons contain heteroatoms—atoms that are not carbon or hydrogen. Most of the derivatives we shall study contain oxygen or nitrogen atoms.

Alkanes Hydrocarbons that contain no rings or multiple bonds are called alkanes. Unbranched alkanes are the basic building blocks of organic molecules; they are named according to the number of carbon atoms in their molecular structure.

Number of C atoms Name Formula1 methane CH4

2 ethane CH3CH3

3 propane CH3CH2CH3

4 butane CH3CH2CH2CH3

5 pentane CH3CH2CH2CH2CH3

6 hexane CH3CH2CH2CH2CH2CH3

7 heptane CH3CH2CH2CH2CH2CH2CH3

8 octane CH3CH2CH2CH2CH2CH2CH2CH3

9 nonane CH3CH2CH2CH2CH2CH2CH2CH2CH3

10 decane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3Note: Memorize these names and corresponding number of C atoms.

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Each name is composed of two parts, a stem or parent name and a suffix. The parent name tells us the number of carbon atoms, and the suffix –ane tells us that the compound is an alkane. For example, hexane tells us that six carbon atoms are joined by single bonds. To draw a picture of hexane’s structure, join six Cs with lines (these lines represent sigma bonds). Every C has four bonds, so every C in the picture must have four lines.

The molecular formula for hexane is C6H14, so fourteen H atoms are bonded to the six carbon atoms. H can form only one bond, so an H is added to the end of each line above to give the following structure.

Every carbon atom requires two H atoms except for the end carbon atoms, which require three hydrogen atoms. If n is the number of carbon atoms in an alkane, then 2n + 2 is the number of hydrogen atoms. The general formula for any alkane is CnH2n + 2. How many H atoms are required for n = 5? Check your answer in the table above.

Obtain a model kit and make a model of hexane. Carbon atoms are black spheres and hydrogen atoms are yellow spheres. Why do the black spheres have four holes and the yellow spheres only one hole? Look at your model. Does the chain of carbon atoms lie in a straight line or in a zigzag pattern?

Skeletal (Bond-Line) Structures The easiest way to show the structure of hexane is with a skeletal structure. Skeletal structures take advantage of the fact that carbon has four bonds and hydrogen one. So, all we need do to depict hydrocarbons is to show the bonding of the carbon atoms. For example, hexane is shown below.

The carbon atoms are located at the ends (1 and 6) and at bends (2, 3, 4 and 5). Because each carbon must have four bonds, there are three H atoms at C1 and

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C6 and two H atoms at C2, C3, C4 and C5. Note that every bond between two carbon atoms is shown as a line. The key to drawing these structures is to know that carbon has four bonds and hydrogen one. Examine your model of hexane and note that the black carbon backbone resembles the structure shown above.

Cycloalkanes Join the two end carbons of your hexane model. The new structure is a continuous loop or ring and is called cyclohexane. The prefix cyclo- means the following number of carbons (hex- = six) is in a ring, and the suffix –ane means there are no multiple bonds in the ring compound. How does the number of carbon atoms, n, compare in hexane and cyclohexane? Write a general formula for cycloalkanes.__________ Three different bond-line depictions of cyclohexane are shown below.

Draw skeletal structures of pentane and cyclopentane.

Sigma () and Pi () Bonds So far, all of the structures you have made contain only single bonds. The first bond made between two carbon atoms is called a bond and the second and third bonds are called bonds. The symbol is the Greek sigma and is pi.

Alkenes Hydrocarbons that contain a carbon-to-carbon double bond (i.e., two bonds, one and one ) are called alkenes. Like alkanes, alkenes are named with a stem that gives the number of carbon atoms but with the suffix –ene to indicate a double bond and a number, if necessary, before the name to indicate the location of the double bond in the carbon chain.

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Number of C atoms Name Formula2 ethene CH2=CH2

3 propene CH2=CHCH3

4 1-butene CH2=CHCH2CH3

5 1-pentene CH2=CHCH2CH2CH3

6 1-hexene CH2=CHCH2CH2CH2CH3

7 3-heptene CH3CH2CH=CHCH2CH2CH3

8 2-octene CH3CH2CH2CH2CH2CH=CHCH3

9 4-nonene CH3CH2CH2CH=CHCH2CH2CH2CH3

10 1-decene CH2=CHCH2CH2CH2CH2CH2CH2CH2CH3

Alkynes Hydrocarbons that contain a carbon-to-carbon triple bond (i.e., three bonds, one and two ) are called alkynes. Like alkenes, alkynes are named with a stem that gives the number of carbon atoms and with a suffix –yne to indicate a triple bond and a number, if necessary, before the name to indicate the location of the triple bond in the carbon chain.

Number of C atoms Name Formula2 ethyne HC≡CH3 propyne HC≡CCH3

4 1-butyne HC≡CCH2CH3

5 2-pentyne CH3CH2C≡CCH3

6 3-hexyne CH3CH2C≡CCH2CH3

7 3-heptyne CH3CH2C≡CCH2CH2CH3

8 2-octyne CH3CH2CH2CH2CH2C≡CCH3

9 3-nonyne CH3CH2CH2CH2CH2C≡CCH2CH3

10 1-decyne HC≡CCH2CH2CH2CH2CH2CH2CH2CH3

Shapes and Bond Angles in Organic Compounds

Tetrahedral Make a model of methane, including hydrogen atoms. We describe the shape of the methane molecule as tetrahedral. A tetrahedral shape is one in which a carbon atom is at the center of a four-sided regular pyramid. In methane, the four hydrogen atoms are at the corners of the pyramid as shown below.

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Tilt your model of methane so you can observe the angle made by the carbon atom and any two hydrogen atoms. This is the tetrahedral angle, which is 109.5o.

Planar Make a model of ethene, including hydrogen atoms. We describe the shape of the ethene molecule as planar. A planar shape is one in which six atoms are coplanar (i.e., lie in the same plane).

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Tilt your model of ethene so you can observe the angle made by one carbon atom and its two hydrogen atoms. This is the planar angle, which is 120o.

Linear Make a model of ethyne, including hydrogen atoms. We describe the shape of the ethyne molecule as linear. A linear shape is one in which four bonded atoms lie in a straight line.

Observe the angle made by any three atoms. This angle is the linear angle, which is 180o.

It is important to be able to associate the three hydrocarbon families with the kind of bonding (single, double or triple) and the geometry (shape and angles) of organic molecules.

Family Carbon Shape AngleAlkane 4 Single bonds Tetrahedral 109.5o

Alkene 1 double bond Planar 120o

Alkyne 1 triple bond Linear 180o

Orbitals in Carbon and Hydrogen

Carbon A carbon atom is made up of protons, neutrons and electrons. The total number of protons (6) equals the total number of electrons (6), so the atom is neutral or uncharged. The protons and neutrons are concentrated in the nucleus

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and do not participate in bonding. The 6 electrons are found outside the nucleus in orbitals. Orbitals are three-dimensional spaces where electrons are found. The electrons in the outermost main shell of carbon can take part in bonding with other atoms; therefore, we are most interested in these electrons. Electrons in the outermost main shell are called valence electrons. Carbon forms four bonds in stable molecules. A carbon atom has four valence electrons, which are found in four valence orbitals. When carbon atoms join to form molecules, some of the orbitals may change shape (hybridize), but each carbon always has four orbitals.

Hybrid Orbitals Carbon can hybridize to make two hybrid orbitals, three hybrid orbitals or four hybrid orbitals. Each bonded carbon atom will always have four orbitals. As we shall see, these three kinds of hybridization are necessary for carbon to make alkynes, alkenes and alkanes. Carbon always has four valence or bonding orbitals. When carbon forms two hybrid orbitals, two orbitals remain unhybridized. When carbon forms three hybrid orbitals, one orbital remains unhybridized. When carbon forms four hybrid orbitals, no orbital remains unhybridized. All hybrid orbitals are shaped like a teardrop. The following graphic show a hybrid orbital.

Unhybridized Orbitals Unhybridized orbitals in carbon are called p orbitals. The shape of a p orbital is shown in the following graphic. A p orbital has two lobes, and hybrid orbitals only one.

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We can explain carbon-to-carbon single bonds, double bonds and triple bonds by the use of the two kinds of orbitals shown above.

Hydrogen A hydrogen atom is made up of a proton and an electron (and isotopes of hydrogen have neutrons). The sole electron is found in a spherical orbital call an s orbital. A graphic of an s orbital is shown below.

Remember, an orbital is a three-dimensional space where electrons are found. Because hydrogen has only one electron, this electron is in the outermost shell and is a valence electron. Valence electrons participate in bonding.

Single Bonds, Double Bonds and Triple Bonds

For discussion purposes, we can consider covalent bonds to form when two orbitals come together or overlap. The following rules will help you understand the bonding in hydrocarbons.

1. Hydrogen always forms one single () bond.2. Carbon always forms four bonds, which may be

a. four single () bonds.b. a double bond ( and ) and two single () bonds.c. a triple bond ( and two ) and one single () bond.d. (rarely) two double bonds (two each and ).

3. Sigma () bonds are formed from the overlap of hybrid or s orbitals.4. Pi () bonds are formed from the overlap of p orbitals.

Single Bonds Carbon-to-carbon single bonds form when two hybrid orbitals overlap end-to-end. Each hybrid orbital contains one electron, so when the orbitals merge, the two electrons are found in the three-dimensional space on a straight line between the two atoms. Think of the hybrid orbitals themselves as electrons. The electrons have opposite spins and hold the atoms together like tiny magnets attracting each other. The following graphic depicts the end-to-end overlap of two hybrid orbitals from two carbon atoms forming a single bond,

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which is also a sigma bond. Each carbon has three other bonds that are indicated by squiggly lines.

Carbon-to-carbon single bond

Carbon to hydrogen single bonds form when a hybrid orbital of a carbon atom overlaps with an s orbital from a hydrogen atom. The graphic below shows a carbon atom forming one single (sigma) bond with hydrogen.

Carbon-to-hydrogen single bond

Double Bonds Carbon-to-carbon double bonds are composed of a bond and a bond. The bond forms on a straight line between the two carbon atoms as above. The bond cannot be in the same space (orbital) because an orbital holds a maximum of two electrons. The bond forms by the side-by-side overlap of two p orbitals. Each p orbital has two lobes, which overlap above and below the bond. The following graphic shows the formation of a double bond. Each carbon must have four bonds. The double bond accounts for two bonds to each carbon, and the squiggly lines indicate the remaining two bonds to each carbon atom.

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Carbon-to-carbon double bond

The figure below show the potential surfaces of two p orbitals coming together to form a bond. The underlying bond is not shown.

Overlap of two p orbitals

Triple Bonds Carbon-to-carbon triple bonds are composed of a bond and two bonds. The bond forms on a straight line between the two carbon atoms as in a single bond and double bond. The first bond forms above and below the bond as in a double bond. The second bond forms perpendicular to the first bond. All carbon-to-carbon bonds form by the end-to-end overlap of hybrid orbitals, and all carbon-to-carbon bonds form by the side-by-side overlap of two unhybridized p orbitals. The following picture shows how the two sets of p

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orbitals overlap. The bond is not shown. Imagine both sets of p orbitals centered on their respective carbon atoms.

The graphic below shows the orbital arrangement in a carbon-carbon triple bond.

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Orbital Arrangements of Carbon in Single, Double and Triple Bonds

Alkanes Consider the structure of ethane. We can determine what kinds of orbitals overlap to make the bonds in ethane by examining its structure.

Both carbon atoms are identical in ethane. One is shown in red for discussion purposes. All four bonds to the red carbon are single () bonds. We learned above that carbon always makes bonds from hybrid orbitals. Thus, four hybrid orbitals are required by the red carbon to form four single bonds. When a carbon atom has four hybrid orbitals, we call that carbon atom sp3 hybridized, and we call each of its four hybrid orbitals sp3-hybrid orbitals. A principle of valence-bond theory is that hybrid orbitals around a given carbon orient as far away from each other as possible. Therefore, the four hybrid orbitals orient toward the corners of a regular tetrahedron. Thus, we can determine the shape of a carbon atom by its hybridization. The orbitals of an sp3-hybridized carbon are tetrahedral and result in methane having a tetrahedral shape as shown above.

Alkenes Consider the structure of ethene.

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The red carbon has four bonds and requires four orbitals, a p orbital for its bond and three hybrid orbitals for its three bonds. A carbon atom with three hybrid orbitals is called an sp2-hybridized carbon, and its three hybrid orbitals are called sp2-hybrid orbitals. The three hybrid orbitals orient as far away from each other as possible, in a plane at 120o angles to each other. The orientation of the hybrid orbitals determines the shape around the carbon atom. The shape is planar. Both carbon atoms of ethene are sp2 hybridized. Therefore, the six atoms of ethyne are coplanar as seen above.

Alkynes Consider the structure of ethyne, which has the common name acetylene.

The red carbon has four bonds and requires four orbitals, two p orbitals for its two bonds and two hybrid orbitals for its two bonds. A carbon atom with two hybrid orbitals is called an sp-hybridized carbon, and its two hybrid orbitals are called sp-hybrid orbitals. The two hybrid orbitals orient as far away from each other as possible, in a line 180o apart. The orientation of the hybrid orbitals determines the shape around the carbon atom. The shape is linear. Both carbon atoms of acetylene (ethyne) are sp hybridized. Therefore, the four atoms of ethane are linear as seen above.

Summary: Carbon has four bonds, which may be or. The first bond made by carbon is always a bond. The second bond of a double bond and the second and third bonds of a triple bond are bonds. Carbon makes bonds with hybrid orbitals and bonds with p orbitals. The number of bonds or hybrid orbitals determines the shape around a carbon atom, because hybrid orbitals orient as far apart as possible. An alkane carbon is sp3 hybridized, has four hybrid sp3 orbitals, forms four bonds 109.5o apart and is tetrahedral. An alkene carbon is sp2 hybridized, has three hybrid sp2 orbitals, forms three bonds 120o apart plus one bond and is planar. An alkyne carbon is sp hybridized, has two hybrid orbitals, forms two bonds 180o apart plus two bonds and is linear.

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Branching Previously, we considered unbranched hydrocarbons. Many hydrocarbons have branches in their structures. A branch, like a branch on a tree, is a carbon chain that veers off the main or longest chain. Consider hexane shown in the structure below.

hexane

Hexane has no branches. Next, consider the structure below. Like hexane, it has six carbon atoms in its main or longest chain. However, it also has a branch at C3.

The parent name of a branched hydrocarbon is the longest continuous chain of carbon atoms. Thus, the structure above is a derivative of hexane. The side chain or branch contains one carbon atom and is a derivative of methane. Thus, the name of the compound represented above is 3-methylhexane. The methyl group contains one carbon and three hydrogen atoms (one less hydrogen atom than in methane).

Partial Structures If we start with methane, CH4, and remove one of its H atoms, we have CH3. CH3 is an incomplete or partial structure because carbon has only three bonds, and carbon always has four bonds in complete structures.

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The name suffix changes from -ane to -yl when one hydrogen atom is removed from the end carbon atom of an alkane. Name the alkyl groups in the following table.

CH3CH2

CH2CH2CH3

CH3CH2CH2CH2CH2

In the name of 3-methylhexane, the number 3 locates the position of the methyl group on the longest chain. We count the number of carbons from each end and give the smaller of the two numbers to the methyl group. In numbering the structure above, we get 3 from the left end and 4 from the right end, so we use 3. In naming, a number is separated from a letter by a hyphen, so the name becomes 3-methylhexane. Numbers are separated from other numbers by commas (i.e., 3,3-dimethylhexane). Each branch on the longest chain is identified by a name and a number.

Isomers Two compounds with the same molecular formula but different structures are called isomers. The carbon-to-carbon skeleton in a hydrocarbon shows the connectivity or constitution of the hydrocarbon. When two hydrocarbon molecules with the same molecular formula differ in their connectivity, we call them constitutional isomers. If they have different formulas, they are not isomers but different compounds. You can draw the structure of very simple hydrocarbons from their molecular formulas, but two or more structures are possible for most formulas.

Draw the structures of CH4, C2H2, C2H6 and C2H4 and name them. These compounds do not have isomers.

Draw the structures of at least three isomers of hexane. Hint: Start with hexane, then make a pentane with a branch, butane with two branches, etc.

Summary of Hydrocarbons We have learned that hydrocarbons contain only carbon and hydrogen and are comprised of alkanes, alkenes, and alkynes. They can have single bonds, double bonds, triple bonds, or rings in their structures. Single, double and triple bonds in hydrocarbons are made up of bonds or bonds. During this course, we shall let the symbol stand for the number of bonds in a structure and r stand for the number of rings in a structure. Shown

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below are the structures and formulas of five different organic compounds. In the space below each structure, indicate how many bonds () and rings (r) are present in each molecule. Then add the two numbers together to get the sum of bonds and rings in each structure.

Derivation of DU Equation We call the sum of bonds and rings in a structure, the number of degrees of unsaturation (DU) in the compound. We see that every time we make a new bond or ring, starting with a hydrocarbon, we must remove two hydrogen atoms. If we let h equal the number of hydrogen atoms in an alkane, we can write h = 2n + 2, because 2n + 2 is the H subscript or number of hydrogen atoms in the general formula of an alkane. Every time we introduce a bond or ring into an alkane, we reduce the number of hydrogen atoms in the formula by two, so for any hydrocarbon h = 2n + 2 – 2 – 2r. Rearrangement of terms gives the hydrocarbon equation below.

Equation 1[Gross, R.A., Jr. Chem. Educator, [Online] 2003 8(1), 13-14; DOI 10.1333/s00897030646a, “An Equation for Degrees of Unsaturation."]Use the hydrocarbon equation to calculate DU ( + r) for each compound above from its molecular formula. Then compare the calculated values to values obtained by counting the bonds and rings in the structures. We shall use the DU equation throughout the course.

Derivation of a Total-Bonds Equation If we look at an alkane’s structure, we can quickly see that the total number of bonds, B, which are all sigma bonds, equals three times the number of carbon atoms, n, plus one. This relationship can be expressed mathematically as shown below.

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B = 3n + 1 Equation 2

Satisfy yourself that this equation works by applying it to several alkanes. Remember that alkanes have only sigma bonds, therefore, the number of pi bonds equals zero, or = 0.

We must make adjustments to the equation for compounds that have pi bonds and rings. The total number of bonds B decreases by one for every pi bond or ring in our compound. Thus, a general equation for the total number of bonds in a hydrocarbon can be derived by subtracting Equation 1 from Equation 2.

B = 3n + 1 – ( + r) = 3n + 1 – (n + 1 – h/2)

B = 2n + h/2 Equation 3 [Gross, R.A., Jr. Chem. Educator, [Online] 2008 13(5), 284-286; DOI 10.1333/s0089708215a, "Derivation and Use of a Total-Bonds Equation."]

Find the number of bonds B in methane and decane by Equations 2 and 3.

Find the number of bonds B in cyclopentane and in cyclohexene by Equation 3.

How many bonds are in an acyclic (no rings) compound of formula C6H6?

Consider how organic molecules are joined together, and derive an equation for the total number of bonds B in any covalent compound from its molecular formula.

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