ORGANIC CHEMISTRY: The Chemistry of Life

Name: ORGANIC CHEMISTRY: The Chemistry of Life
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Description: ORGANIC CHEMISTRY: The Chemistry of Life

ORGANIC CHEMISTRY: The Chemistry of Life
© 2012 Pearson Education, Inc.

© 2012 Pearson Education, Inc.
Organic Chemistry Organic chemistry is the chemistry of carbon compounds. Carbon has the ability to form long chains. Without this property, large biomolecules such as proteins, lipids, carbohydrates, and nucleic acids could not form. © 2012 Pearson Education, Inc.

Structure of Carbon Compounds
There are three geometries or hybridization states or found on each carbon in any organic compounds: Sp3 hybridized - tetrahedral sp2 hybridized - trigonal planar sp hybridized - linear © 2012 Pearson Education, Inc.

Organic Compounds: Alkanes and Cycloalkanes
CHAPTER 2 Organic Compounds: Alkanes and Cycloalkanes

Formulas Lewis structures of alkanes look like this They are also called complete structural formulas. They are often not convenient, though…, Complete Structural Formula Condensed Structural Formulas © 2012 Pearson Education, Inc.

Formulas …so more often condensed formulas are used. Because some organic molecules can consist of thousands of atom an even more abbreviated Skeletal Formula was devised. © 2012 Pearson Education, Inc.

Drawing Chemical Structures
Chemists use shorthand ways for writing structures Condensed structures: C-H and C-C single bonds aren't shown but understood If C has 3 H’s bonded to it, write CH3 If C has 2 H’s bonded to it, write CH2; and so on. The compound called 2-methylbutane, for example, is written as follows: Horizontal bonds between carbons aren't shown in condensed structures—the CH3, CH2, and CH units are simply but vertical bonds are added for clarity Complete Structural Formula

Skeletal Structures C’s are not shown. They are assumed to be at each intersection of any two lines (bonds) and at end of each line H’s bonded to C’s aren't shown –Since carbon always has a valence of 4, we mentally supply the correct number of H’s by subtracting the # of bonds shown from 4. All atoms other than C and H are shown See next slide for examples

Multiple Bonds In condensed formulas double and triple bonds are drawn as they would be in a Lewis structure showing two dashes for a double bond and three dashes for a triple bond

Families of Organic Compounds
Organic compounds can be grouped into families by their most important structural feature – by their: Functional Groups

Functional Groups A Functional Group is an atom or collection of atoms that imparts characteristic chemistry to whatever hydrocarbon skeleton that it is bonded to. The functional group reacts in the same way, independent of the rest of the molecule For example, the double bonds in simple and complex alkenes react with bromine in the same way.

Common Rxns of the Double Bond Functional Group

Survey of Functional Groups
The inside cover of your text lists the organic functional groups. You must memorize them. As you learn about them in each chapter it will be easier to recognize them The functional groups affect the reactions, structure, and physical properties of every compound in which they occur

For Ease of Study the Functional Groups can be grouped into a few types based upon their common structural features

Types of Functional Groups: Multiple Carbon–Carbon Bonds
Alkenes have a C-C double bond Alkynes have a C-C triple bond Arenes or Aromatics have special bonds that are represented as alternating single and double C-C bonds in a six-membered ring

Functional Groups with Carbon Singly Bonded to an Electronegative Atom
Alkyl halide: C bonded to halogen (C-X) Alcohol: C bonded O of a hydroxyl group (COH) Ether: Two C’s bonded to the same O (COC) Amine: C bonded to N (CN) Thiol: C bonded to SH group (CSH) Sulfide: Two C’s bonded to same S (CSC) In all of these functional groups the bond between Carbon and the electronegative atom is polar, with partial positive charge on C (+) and partial negative charge () on electronegative atom

Groups with a Carbon–Oxygen Double Bond (Carbonyl Groups)
Aldehyde: one hydrogen bonded to C=O Ketone: two C’s bonded to the C=O Carboxylic acid: OH bonded to the C=O Ester: O-C bonded to the C=O Amide: N-C and/or N-H bonded to the C=O Acid chloride: Cl bonded to the C=O In all of these functional groups the Carbonyl C has a partial positive charge (+) and the Carbonyl O has partial negative charge (-).

Alcohols Alcohols contain one or more hydroxyl groups, —OH. They are named from the parent hydrocarbon; the suffix is changed to -ol and a number designates the carbon to which the hydroxyl is attached. © 2012 Pearson Education, Inc.

Circle and name the functional group(s) in the following molecules.
amide amine Carboxylic acid alkene ester arene alkene alkene ketone alcohol

Circle and name the functional groups
alcohol amine arene

Circle and name the functional groups
Carboxylic acid arene Alkane

The Functional Group that we will focus on in this chapter is the Alkane
Alkanes: Compounds with C-C single bonds and C-H bonds only The general formula for an alkane with no rings in it must be CnH2n+2 where the number of C’s is n Alkanes are said to be saturated with hydrogens (no more can be added) They are also called aliphatic compounds or parrafins n-

This is a Saturated Animal Fat-
a Triglyceride

The Names for the first 10 Alkanes must be committed to memory
No. of Carbons Formula Name (CnH2n+2) 1 Methane CH4 2 Ethane C2H6 3 Propane C3H8 4 Butane C4H10 5 Pentane C5H12 6 Hexane C6H14 7 Heptane C7H16 8 Octane C8H18 9 Nonane C9H20 10 Decane C10H22

Alkane Isomers When we get to Butane, C4H10, we find that there are two different structures that can share the same formula; These are: n-Butane and Isobutane or 2-methylpropane. They are isomers of one another (CH3)3CH CH3CH2CH2CH3 n-

There are different kinds of Isomers
Isomers that differ in how their atoms are arranged in chains are called constitutional isomers Compounds other than alkanes can be constitutional isomers of one another Constitutional isomers can be skeletal, functional group or positional

. If we continue to build succeedingly larger alkanes according to the general formula CnH 2n+2, we will discover that the number of isomers for each one increases greatly.

The Need for a System of Nomenclature
It is obvious that the existence of such vast numbers of isomers (75 for Decane) require a system of nomenclature that can identify any one of these. Before enumerating the rules for nomenclature, there are two items that we must cover. Classification of Carbon atoms Classification of Hydrogen atoms

Classification of Carbon Atoms
A carbon atom may be classified by identifying the number of other carbon atoms that it is bonded to. Note R is used here and throughout the notes on organic chemistry to represent a general hydrocarbon group.

We often use these terms when speaking, therefore, their meanings
We often use these terms when speaking, therefore, their meanings must become second nature. For example;

Classification of Hydrogen Atoms
Hydrogens are classified as primary (1°), secondary (2°) or tertiary (3°) depending upon the class of carbon that they are bonded to. How many primary, secondary and tertiary hydrogens are in the following; CH3CH(CH3)CH2CH(CH3)2 12, 1°’s 2, 2°’s 2, 3°’s

Classification of Hydrogens

Naming Alkanes 2,3-dimethylpentane
Alkanes are named by a process that uses Prefix-Parent-Suffix branching groups are in longest chain? 2,3-dimethylpentane

Naming Alkyl Groups These alkyl groups will later appear as branches that hang off the longest carbon chain of larger organic molecules. Their names must be committed to memory.

Rules for Naming Alkanes
Identify the longest continuous carbon chain = parent name Number the carbons of the longest chain starting from the end that gives the smallest number for the first branch point. Name the molecule by identifying the name of each branch and its position on the longest carbon chain, followed by the name of the parent.

Find the longest continuous carbon chain and determine the name of the parent name
3-methylhexane 4-ethyl-3-methylheptane

Number the Carbon Atoms in the longest carbon chain- start at the end that gives the smallest number for the first branch

Number the carbons in the longest carbon chain
3-ethyl-4,7-dimethylnonane

Identify and Number the Substituents
4-ethyl-2,4-dimethylhexane

Write the name as a single word

Alternative Method for Naming Complex Branches
When naming the more complex branches (branches that have their own branches), the branch carbon that is directly attached to the main chain is labelled as the #1 branch carbon and the branch is then named as if it were a compound itself. However the complex branch name still ends in the suffix –yl. When named this way, the complex branch name is always placed within parenthesis. Consider the following complex branches.

(1-methylpropyl) ( 2-methylpropyl) ( 1,1-dimethylethyl)

Properties of Alkanes Alkanes are called paraffins (from the Greek “para affinis” meaning low affinity because they have a very low reactivity They will burn in a flame, producing carbon dioxide, water, and heat and… They react with Cl2 in the presence of light to replace H’s with Cl’s (not controlled)

Physical Properties Boiling points and melting points increase as size of alkane increases Forces between molecules (intermolecular forces are London Dispersion forces. These are weak but increase with increasing molecular weight

Cycloalkanes: Cis-Trans Isomerism
Cycloalkanes or alicyclic compounds (aliphatic cyclic) are rings of carbon atoms that have the general formula CnH2n In many respects, the chemistry of cyclalkanes mimic that of the noncyclic alkanes. They are all nonpolar and chemically inert to most reagents. The main difference between cycloalkanes and noncyclic alkanes is the lack of complete rotation about the carbon to carbon ring bond. This decrease in freedom of rotation about the carbon to carbon bond is most obvious in the small ring cycloalkanes For example, cyclopropane cannot have any carbon to carbon bond rotation without breaking the ring. Cyclopropane must be a flat, planar molecule with a rigid structure

Cis-Trans Isomerism in Cycloalkanes
Rotation about C-C bonds in cycloalkanes is limited by the ring structure Rings have two “faces” and substituents are labeled as to their relative facial positions There are two different 1,2-dimethyl-cyclopropane isomers, one with the two methyls on the same side (cis) of the ring and one with the methyls on opposite sides (trans)

Cycloalkanes Some two dimensional representations of cycloalkanes
cyclobutane cyclopropane cyclopentane cyclohexane

Complex Cycloalkanes Naturally occurring materials contain cycloalkane structures Examples: chrysanthemic acid (cyclopropane), prostaglandins (cyclopentane), steroids (cyclohexanes and cyclopentane)

Naming Cycloalkanes Count the number of carbon atoms in the ring and the number in the largest substituent chain. If the number of carbon atoms in the ring is equal to or greater than the number in the substituent, the compound is named as an alkyl-substituted cycloalkane For an alkyl- or halo-substituted cycloalkane, start at a branch and call its ring carbon, C1 ,and number the substituents on the ring so that the second substituent has as low a number as possible. Number the substituents and write the name See text for more details and examples

Stereoisomers Compounds with atoms connected in the same order but which differ in three-dimensional orientation, are stereoisomers The terms “cis” and “trans” should be used to specify stereoisomeric ring structures Recall that constitutional isomers have atoms connected in different order

The Shapes of Molecules
I. Stereochemistry: the branch of chemistry concerned with the three dimension shapes of molecules The most stable shape of Decane.

A molecule may assume different shapes, called conformations, that result from rotation about a carbon-carbon single bond. Although there are many possible conformations available to a particular molecule; each molecule will spend most of its time in its most stable conformation. The most stable conformation for any molecule is the one that minimizes the mutual repulsion of bonded electron clouds on adjacent carbons.

Representing Conformations
Sawhorse representations: these view the C-C bond from an oblique angle and indicate spatial orientations by showing all the C-H bonds. Newman projections: these site along a particular C-C bond and represent the two carbon atoms by a single circle. Substituents on the front carbon are represented by lines going to the center of the circle, and substituents on the rear carbon are indicated by lines going to the edge of the circle.

Conformations of Ethane – Torsional Strain Energy
Rotation about the C-C bond in ethane is not exactly free. There is a slight energy barrier (12 kJ/mol) to this rotation. This barrier stems from the fact that certain conformers have a higher energy content (are less stable) than others. The highest energy, least stable conformer is the eclipsed conformer. In this conformer all six C-H bonds are as close as possible. Since the energy barrier is 12 kJ/mol and we can see from the highest energy eclipsed conformer that this is due to three H,H eclipsing interactions, then we can assign a value of 4 kJ/ mol for each H,H eclipsing interaction. This increased energy due to eclipsing interactions is called torsional strain and is one kind of strain energy. Torsional strain is due to mutual repulsion between electron clouds as they pass by each other in eclipsed conformers

Staggered Conformation of Ethane
The lowest energy, most stable conformer is the staggered conformer. In this conformer, all six C-H bonds are as far apart as possible

Ethane’s Conformations
There barrier to rotation between conformations is small (12 kJ/mol; 2.9 kcal/mol) The most stable conformation of ethane has all six C–H bonds away from each other (staggered) The least stable conformation has all six C–H bonds as close as possible (eclipsed) in a Newman projection – energy due to torsional strain

Conformations of Propane – Steric Strain Energy
The barrier to free rotation about carbons #2 and #3 is 14 kJ/mol. Inspection of the highest energy eclipsed conformer indicate that this strain is due to two H,H interactions and one H,C interaction. We have seen in ethane that each H,H interaction accounts for approximately 4 kJ/mole of strain energy. This means that the C,H interaction must account for 6kJ/mole of strain energy. The C,H strain energy of propane is due to torsional and steric strain. Steric strain results from two atoms or groups attempting to occupy the same space at the same time.

4.3 Conformations of Butane
The barrier to free rotation about C2-C3 in butane is 19kJ/mole. Inspection of the highest energy eclipsed conformation indicates that the torsional strain is due to two H,H interactions and one C,C interaction. This allows us to calculate a value of 11 kJ/ mole for the methyl, methyl eclipsing interaction. Consider the plot of P.E. vs rotation about C2 - C3 in butane and notice that there are two different staggered conformers that do not have the same energy and two different eclipsed conformers that do not have the same energy. We know that the highest energy eclipsed conformer has a total strain of 19 kJ/mole. 3.8 kJ/mole 19 kJ/mole 0 kJ/mole

The Gauche Butane Conformer
The energy of this conformer is 3.8 kJ/mol higher in energy than the most stable,anti conformer even though it has no eclipsing interactions. The strain energy of this conformer results from the fact that the H’s of both CH3 groups are attempting to occupy the same space at the same time. This type of strain is called… Steric Strain

Stability of Cycloalkanes: The Baeyer Strain Theory
In 1885, Baeyer proposed a theory to explain the apparent lack of cyclic alkanes having certain ring sizes. More specifically only 5 and 6 membered cycloalkane rings were known but smaller and larger rings could not be prepared. Baeyer theorized that these could not be prepared because their bond angles would necessarily deviate from the preferred sp3 bond angle of degrees. This deviation would cause such angle strain that the rings would be too unstable to exist.

Bayer’s Proposed Bond Angle Strain
Compound Structure Baeyer Bond Angle Angle Strain Cyclopropane 60 degrees 109-60=49 Cyclobutane 90 degrees 109-90=19 Cyclopentane 108 degrees =1 Cyclohexane 120 degrees = -11 Baeyer concluded that cyclopropane would be the most strained followed by cyclobutane. Cyclopentane would be strain free while cyclohexane would show a substantial amount of strain energy. Rings larger than cyclohexane would be impossibly strained and not capable of existing.

Measurements of Energy Strain in a Cyclic Compound
Heats of combustion can be used to measure the total amount of energy strain in a compound. The notion here is that the more strained a compound, the higher is its energy content and the more heat delivered per CH2 unit upon combustion to CO2 + H2O. Alkane + O CO2 + H2O + Heat

Bayer’s Theory Busted Heats of combustion data indicate that Baeyer's theory was not fully correct. Cyclopropane and cyclobutane are quite strained but cyclopentane is more strained then first predicted while cyclohexane is less strained. For larger rings, there is no regular increase in strain and rings of more than 14 carbons are strain free. Why was Baeyer's theory incorrect? Baeyer assumed that all cycloalkanes are flat when in fact most adopt a puckered 3-D conformation. Furthermore, he did not consider the contribution of torsional strain to the overall strain energy of a molecule.

The Nature of Ring Strain
Rings larger than 3 atoms are not flat Cyclic molecules can assume nonplanar conformations to minimize angle strain and torsional strain by ring-puckering

Summary: Types of Strain
Angle strain - expansion or compression of bond angles away from the preferred 109.5 Torsional strain - eclipsing of bonds on neighboring atoms Steric strain - repulsive interactions when two atoms or groups bump in to one another

Conformations of some Cycloalkanes
3-membered ring must have planar structure Symmetrical with C–C–C bond angles of 60° Requires that sp3 based bonds are bent (and weakened) All C-H bonds are eclipsed

Conformations of Cyclobutane and Cyclopentane
Flat cyclobutane has less angle strain than cyclopropane but much more torsional strain because of its larger number of ring hydrogens Consequently, cyclobutane is slightly bent out of plane - one carbon atom is about 25° above The bend increases angle strain but decreases torsional strain

Cyclopentane Planar cyclopentane would have no angle strain but very high torsional strain Actual conformations of cyclopentane are nonplanar because this reduces the torsional strain somewhat. Four carbon atoms are in a plane The fifth carbon atom is above or below the plane – looks like an envelope

Conformations of Cyclohexane
Cyclohexane compounds are the most important of all cycloalkanes because of their wide occurrence in nature. Cyclohexane is a strain free cycloalkane because of a 3-D conformation that relieves all strain. The C,C bond angles of this chair confirmation are all ~ 109 degrees and the conformation displays no H,H eclipsing strain

How to Draw Cyclohexane

Axial and Equatorial Bonds in Cyclohexane
The chair conformation has two kinds of positions for substituents on the ring carbons: axial positions and equatorial positions Chair cyclohexane has six axial hydrogens perpendicular to the ring (parallel to the ring axis) and six equatorial hydrogens near the plane of the ring

Axial and Equatorial Positions
Each carbon atom in cyclohexane has one axial and one equatorial hydrogen Each face of the ring has three axial and three equatorial hydrogens in an alternating arrangement

Drawing the Axial and Equatorial Hydrogens

Conformational Mobility of Cyclohexane
Chair conformations readily interconvert, resulting in the exchange of axial and equatorial positions by a ring-flip

Bromocyclohexane When bromocyclohexane ring-flips the bromine’s position goes from equatorial to axial and so on

Conformations of Monosubstituted Cyclohexanes
The two conformers of a monosubstituted cyclohexane are not equal in energy The equatorial conformer of methyl cyclohexane is more stable than the axial by 7.6 kJ/mol

Conformational Analysis of Disubstituted Cyclohexanes
The most stable conformer is the one that has the largest group in the equatorial position.

Conformational Analysis of Disubstituted Cyclohexanes
In disubstituted clohexanes the steric effects of both sbstituents must be taken into account in both conformations Be careful here. Remember that there are four conformational isomers of 1,2 dimethyl cyclohexane. There are two cis cinformers related by a ring flip and two trans related by a ring flip. Your job is to identify the one with the least strain energy. The most stable one Also remember that each face has alternating axial and equatorial positions a e e e a a e a a e e a bottom top botton

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