Introduction to Organic Chemistry

Introduction to Organic Chemistry Yes!! I can’t wait!!! I hear everyone fails this in college!!!

Intro - Organic Molecules • Living things are composed of organic molecules, which means that they contain carbon • carbon has four electrons in outer shell which can bond with other atoms • carbon can be linked to other carbons or atoms such as hydrogen (H), oxygen (O) and nitrogen(N) • long links of these carbons can form into chains or rings • Some organic molecules ONLY contain linked carbons and hydrogen ---->hydrocarbons (ex: methane) • living organisms tend to be composed of very long and unreactive carbon chains (unlike methane, which is very reactive!)

Intro – Functional Groups • In organic chemistry, molecules with similar properties are grouped together • These all have similar groups of atoms, and these groups of atoms are called functional groups • Functional groups can provide physical and chemical properties such as polarity and acidity (ex; carboxyl, -COOH, is a weak acid) • Most reactions in living organisms involves the transfer of a functional group from one molecule to another • The following is a list of common functional groups • OHHydroxyl • COCarbonyl • COOHCarboxyl • NH2Amino • SHSulfhydryl • PO4 Phosphate • CH3Methyl YOU MUST MEMORIZE THIS LIST!!!

Intro – Functional Groups

Intro - Macromolecules • Construction of Macromolecules • many macromolecules are polymers, which means that they are constructed of many linked identical or similar subunits • How are macromolecules made? Remove an OH from one molecule, and an H from another molecule • this requires energy • it is called dehydration synthesis (do you see the water above?!) • in living organisms, enzymes assist in these reactions • Macromolecules are disassembled in the opposite way, by adding a water molecule (OH added to one, H to another subunit) • this releases energy • a reaction of this type is called a hydrolysis

Intro - Dehydration Synthesis

Hydrocarbons - Naming • Compounds containing just carbons and hydrogens are the most basic compounds encountered in organic chemistry. • hydrocarbons. • can be divided into three groups: • those containing just single bonds • those containing one or more double bonds • those containing one or more triple bonds. • Before discussing how to name these compounds, it is instructive to examine how they are represented by chemists.

Drawing Hydrocarbons • Recall - carbon makes four bonds and had the tetrahedral geometry • only two bonds can occupy a plane simultaneously. • The other two bonds point in back or in front of the plane. • In order to represent the tetrahedral geometry in two dimensions • solid wedges are used to represent bonds pointing out of the plane of the drawing toward the viewer • dashed wedges are used to represent bonds pointing out of the plane of the drawing away from the viewer • Consider the following representation of the molecule methane: • Two dimensional representation of methane

Drawing Hydrocarbons • it can be time-consuming to write out each atom and bond individually. • hydrocarbons can be represented in a shorthand notation called a skeletal structure. • only the bonds between carbon atoms are represented. • Individual carbon and hydrogen atoms are not drawn • bonds to hydrogen are not drawn. • If the molecule contains just single bonds; drawn in a "zig-zag" fashion. • This is because in the tetrahedral geometry all bonds point as far away from each other as possible, and the structure is not linear. representations of the molecule propane: • Full structure of propane Skeletal structure of propane

Drawing Hydrocarbons • Only the bonds between carbons have been drawn, and these have been drawn in a "zig-zag" manner. • no evidence of hydrogens in a skeletal structure. • in the absence of double or triple bonds, carbon makes four bonds total, the presence of hydrogens is implicit. • Whenever an insufficient number of bonds to a carbon atom are specified in the structure, it is assumed that the rest of the bonds are made to hydrogens. • For example: • if the carbon atom makes only one explicit bond, there are three hydrogens implicitly attached to it. • If it makes two explicit bonds, there are two hydrogens implicitly attached, etc. • Two lines are sufficient to represent three carbon atoms. • It is the bonds only that are being drawn out & it is understood that there are carbon atoms (with three hydrogens attached!) at the terminal ends of the structure.

Alkane nomenclature • When hydrocarbons contain only single bonds, they are called alkanes. • Alkanes are named using a prefix for the number of carbon atoms they contain, followed by the suffix -ane. Number root example Structure • 1 meth- methane (see board) • 2 eth- ethane • 3 prop- propane • 4 but- butane • 5 pent- pentane • 6 hex- hexane • 7 hept- heptane • 8 ox- oxane • 9 non- nonane

Alkane nomenclature • Alkane nomenclature is straightforward; • difficulties come if one of the hydrogen or carbon atoms on the molecule is replaced by another atom or group. • When this takes place, the group which replaces the hydrogen or carbon is called a substituent. • Let's consider the situation in which one of the hydrogen atoms on an alkane has been replaced by another alkane. • Consider the following molecule, 3-methypentane:

Alkane nomenclature • Consider the following molecule, 3-methypentane • Long chain of five carbon atoms at the top of the image. • If this were all that composed the molecule, it would simply be called pentane. • However, one of the hydrogens on the carbon third from the end has been replaced with an alkane, specifically methane. • How are we to name this molecule?

Alkane nomenclature - Rules • First, we identify the longest chain of carbon atoms. We name this alkane. It will serve as the root name for the molecule. In the example above, the root name is pentane. • Next, we number the carbon atoms, starting at the end that gives the substituent the lowest number. In the example above, we can count from either end and arrive at 3 for the substituent. • Next, we name the substituent as if it were an independent alkane. However, we replace suffix -ane with -yl. This name will serve as the prefix. In the example above, methane is the substituent, so we call it methyl. • The compound is named "number-prefixrootname". In the example above, the name is 3-methylpentane

Alkane nomenclature - Rules • What happens if the alkane has more than one substituent? • In this case, the rules above are followed, and the carbons on the longest chain are numbered to give the lowest number possible to one of the substituent. • The substituents are then all named in the prefix (e.g. 2-ethyl,3-methyl). • If more than one substituent is attached to the same carbon atom, the number of that carbon atom is repeated to indicate the number of substituents and the prefixes di- (2) or tri- (3) are used. • If there are more than one substituent on different carbon atoms, the prefixes are ordered alphabetically (e.g. ethene before methane). • The prefixes di- and tri- are ignored when considering alphabetical order. Consider the following compound:

Alkane nomenclature • The longest carbon chain has seven carbon atoms, so the root name is heptane. • Numbering from the right gives the lowest number to the first substituent. • There are two methyl substituents at the second carbon atom, so we use the prefix 2,2-dimethyl. • There is another substituent on the fourth carbon atom, so we use the prefix ethyl. • Ethyl comes before methyl alphabetically, so we name the compound 4-ethyl-2,2-dimethylheptane.

Alkene Nomenclature • Alkenes are hydorcarbons containing one or more double bonds. • Alkenes are named using the same general naming rules for alkanes, except that the suffix is now -ene. There are a few other small differences: • The main chain of carbon atoms must contain both carbons in the double bond. • The main chain is numbered so that the double bond gets the smallest number. • Before the root name, the number of the carbon atom at which the double bond starts (the smaller number) is written. • If more than one double bond is present, the prefixes di-, tri-, tetra-, etc. are used before the -ene, and (strangely) the letter "a" is added after the prefix for the number of carbon atoms.

Alkyne Nomeclature • Hydorcarbons containing one or more triple bonds are called Alkynes. • Alkynes are named using the same general procedure used for alkenes, replacing the suffix with -yne. • If a molecule contains both a double and a triple bond, the carbon chain is numbered so that the first multiple bond gets a lower number. • If both bonds can be assigned the same number, the double bond takes precedence. • The molecule is then named "n-ene-n-yne", with the double bond root name preceding the triple bond root name • (e.g. 2-hepten-4-yne).

Functional Group Nomenclature • Alkanes are extremely unreactive. • Carbon-carbon and carbon-hydrogen bonds are among the most stable bonds in chemistry • alkanes serve as a backbone or template on which unreactive carbon or hydrogen atoms can be replaced by substituents consisting of more reactive atoms or groups of atoms. • A substitient consisting of an atom or group of atoms other than carbons and hydrogens is called a functional group. • Functional groups are significant because they are the part of the molecule that undergoes reactions. • One functional group may change into another one, or a functional group might react with a separate molecule to build up a larger structure. • Functional groups are the essential "reacting units" in organic chemistry.

Functional Group Nomenclature • We have already encountered two functional groups. The double bonds in alkenes and the triple bonds in alkynes are able to undergo reactions that the single bonds in alkanes cannot. • There are several other significant functional groups, summarized in the table below. Note that in organic chemistry, the letter "R" represents any alkane, and the letter "X" represents any halogen. • Functional group Structure • Alkyl halide R-X • Alcohol R-OH • Ether R-O-R • Amine NR3

Naming Alkyl Halides • One of the simplest functional groups is the alkyl halide. • In an alkyl halide, one of the hydrogen atoms in an alkane has been replaced by a halogen. • What are halogens again? • Alkyl halides are easy to name; • name of the alkane is preceded by the number of the carbon on which the halogen is substituted and the name of the halogen, • modified so that -ine is replaced by -o (e.g. 2-bromopropane). • If a molecule also contains a multiple bond, numbers are assigned to give the lowest number to the first functional group. In the event of a tie, the lowest number goes to the multiple bond.

Naming Alcohols • The alcohol is a very common functional group and a very easy one to name. • The molecule is named as if it were an alkane (or alkene or alkyne) • except that the suffix -ane is replaced by -ol • and the number of the carbon atom on which the -OH group is located is placed before the name of the compound (e.g. 2-butanol). • The alcohol functional group takes precedence over alkyl substituents, multiple bonds, and halides and always gets the lowest number.

Naming Ethers • An ether is a molecule consisting of two alkyl groups connected to an oxygen atom. • Ethers are named by considering one alkyl group (the shorter one) plus the oxygen atom to be a substituent and the other alkyl group (the longer one) to be an alkane. • The alkyl group plus oxygen atom is called an "alkoxy" substituent and is named by replacing -ane suffix from the alkane with -oxy (e.g. methane becomes methoxy). • The allkoxy substituent gets priority over alky and halide substituents, but not over alcohols, which will get the lower number.

Naming Amines • An amine is a derivatives of the molecule ammonia, NH3, in which one or more of the hydrogens has been replaced by an alkyl substitutent (R group). • Amines are named by treating the amino group as a substituent and giving it the name "amino" (e.g. 2-aminobutane). • If multiple hydrogens have been replaced by alkyl substituents, then these alkyl substituents are stated before the word "amino" (e.g. 2-dimethylaminobutane).

Cycloalkanes • The alkanes we have studied so far have been of two types: linear and branched. There is a third type of alkane in which the molecule does not have ends but instead forms a ring. • These molecules are called cycloalkanes Figure 1: Skeletal structure of cyclohexane, a cycloalkane

Cycloalkanes • Stable cycloalkanes cannot be formed with carbon chains of just any length. • Recall that in alkanes, carbon adopts the tetrahedral geometry in which the angles between bonds are 109.5°. • For some cylcoalkanes to form, the angle between bonds must deviate from this ideal angle, an effect known as angle strain. • Additionally, some hydrogen atoms may come into cloeser proximity with each other than is desirable (become eclipsed), an effect called torsional strain. • These destabilizing effects, angle strain and torsional strain are known together as ring strain.

Cycloalkanes • The smaller cycloalkanes, cyclopropane and cyclobutane, have particularly high ring strains because their bond angles deviate substantially from 109.5° and their hydrogens eclipse each other. • Cyclopentane is a more stable molecule with a small amount of ring strain, while cyclohexane is able to adopt th perfect geometry of a cycloalkane in which all angles are the ideal 109.5° and no hydrogens are eclipsed; it has no ring strain at all. • Cycloalkanes larger than cyclohexane have ring strain and are not commonly encountered in organic chemistry.

Cyclohexane • Most of the time, cyclohexane adopts the fully staggered, ideal angle chair conformation (Figure 2). • In the chair conformation, if any carbon-carbon bond were examined, it would be found to exist with its substituents in the staggered conformation and all bonds would be found to possess an angle of 109.5°.

Methylcyclohexane • Methylcyclohexane is cyclohexane in which one hydrogen atom is replaced with a methyl group substituent. • Methylcyclohexane can adopt two basic chair conformations: one in which the methyl group is axial, and one in which it is equatorial. • Methylcyclohexane strongly prefers the equatorial conformation. • In the axial conformation, the methly group comes in close proximity to the axial hydrogens, an energetically unfavorable effect known as a 1,3-diaxial interaction • Thus, the equatorial conformation is preferred for the methyl group. In most cases, if the cyclohexane ring contains a subsituent, the substituent will prefer the equatorial conformation.

OUCH!!! • Stop please stop my head is hurting and I am pretty sure my brain is bleeding? • Do we really have to know all of this for the test? • Will I really have to know all of this for the future in organic chemistry? • Can I quit now and just become a Kindergarten teacher?

Introduction to Organic Chemistry