Week 1 Introduction to Organic Chemistry Workbook - Monash 2024 PDF

7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 Week 1: Introduction to Organic Chemistry - workbook Site: Monash Moodle1 Printed by: Kal...

7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 Week 1: Introduction to Organic Chemistry - workbook Site: Monash Moodle1 Printed by: Kaltham Alzaabi Unit: CHM1022 - Chemistry II - S2 2024 Date: Friday, 26 July 2024, 6:05 PM Book: Week 1: Introduction to Organic Chemistry - workbook https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 1/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 Table of contents 1. Pre-workshop material 1.1. Introduction to Hydrocarbons 1.2. Alkanes 1.3. Three-dimensional structure of alkanes 1.4. Alkenes and Alkynes 2. Summary 3. Preparation quiz 4. Online lectures 5. Mechanisms 6. Workshops https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 2/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 1. Pre-workshop material Organic chemistry is the chemistry of carbon and compounds of carbon. These commonly are materials with hydrogen, carbon, oxygen, nitrogen. We study the structure of these materials (Shapes). We study the properties of these materials (What can they do?). We study how they react to make new materials (Can we use them to make other molecules?). The molecules of your life are largely organic. This is hardly surprising when you realise that the most abundant elements on earth are organic, namely hydrogen, carbon, oxygen and nitrogen. Below is a period table with the size of each element roughly distorted to match its abundance. Please read Sections 2.2-2.3 of Chemistry, Blackman et al. (4th ed.). Please read Chemistry: Atoms First (2019), Chapter 21.1. https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 3/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 1.1. Introduction to Hydrocarbons Hydrocarbons are the simplest form of organic molecule consisting of only carbon and hydrogen. There are many forms of hydrocarbon, most of which are derived from crude oil. When a carbon is hybridised sp3 the carbons form 4 sigma bonds and we describe them as saturated. If they are sp or sp2 hybridised they can form C-C multiple bonds (double or triple), and they are classified unsaturated (I think of them as not being saturated with hydrogens). Unsaturated hydrocarbons are: alkenes (double bond) and involve 2 sp2 carbons, alkynes (triple bond) that involve 2 sp hybridised carbons, or arenes (which will be discussed later in this unit). This is summarised below. Figure 1: Hydrocarbons In Figure 1, the molecules of ethane, ethene and ethyne have both carbon and hydrogen depicted. This is a line bond structural drawing. In organic chemistry, we tend to draw our molecules as condensed structural drawings, similar to the benzene molecule in Figure 1. This makes drawing simpler, however you need to remember some key points: The line represents a Carbon-Carbon sigma bond. The vertex (point where two lines meet) represent a Carbon atom. All other elements will have their chemical symbol (e.g. N for nitrogen) Hydrogens bonded to the carbons are not drawn in (mainly). But you need to remember that they are still there. Remember, carbon most commonly has 4 bonds - thus if a vertex has two lines to other carbons, then the two remaining bonds are to hydrogen (see below for some examples). https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 4/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 Functional group introduction While simple hydrocarbons are important it is more common to have functionalised hydrocarbons. That is, hydrocarbons with various functional groups attached. A functional group is a series of atoms that behave in a common way. NOTE: THIS LIST OF FUNCTIONAL GROUPS IS HERE TO HELP YOUR LEARNING. PLEASE DO NOT MEMORISE THEM. AS WE STUDY MORE OF THEM YOU WILL START TO REMEMBER THE ONES THAT MATTER. Functional groups: This is a list of some common functional groups in chemistry. Being familiar with their structure and name will help your studies. Name General structure example name Alcohol ethanol Ether diethylether Amine butylamine Alkyl halide 1-chlorobutane Carbonyl compounds ethanal aldehyde (common name: acetaldehyde) propanone ketone (common name: acetone) ethanoic acid carboxylic acid (common name: acetic acid) ester propyl benzoate N‑methylcyclopropanecarboxamide amide https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 5/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 Please read Sections 16.1- 16.3 of Chemistry, Blackman et al. (4th Ed.) https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 6/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 1.2. Alkanes Alkanes are entirely made of single bonded carbons, with the simplest member being methane. 1.1 Naming of Hydrocarbons Chemistry has its own language that allows accurate communication. As your studies progress this new tongue will become natural. The naming rules will be presented in the yellow boxes, similar to below, as we progress through the course. NOTE: THE NAMING RULES FOR HYDROCARBONS ARE HERE TO HELP YOU APPRECIATE HOW NAMES ARE GENERATED. PLEASE DO NOT MEMORISE THEM. AS WE STUDY MORE OF THEM YOU WILL START TO REMEMBER THE ONES THAT MATTER. Naming #1: Alkanes All molecule names that have the –ane suffix means they are all alkanes. The prefixes have various origins and are used to define how many carbons are present. We will use these prefixes again and again and again…so they are worth trying to remember. prefix Number of Origin carbons Meth- 1 Eth- 2 Complex, but interesting, if you like studying the origin of Prop- 3 words But- 4 Pent- 5 Hex- 6 Hept- 7 All from Greek, you may have experienced these prefixes Oct- 8 when studying geometric shapes. Non- 9 Dec- 10 As we increase the number of carbon & hydrogen atoms on the hydrocarbon molecule, the properties of the molecule changes, with melting point, boiling point and density all increasing. This is a result of increased intermolecular forces between the molecules. Table 16.1 below clarifies this concept further, where the melting point, boiling point and density of the first 10 straight chain alkanes are listed. For revision on intermolecular forces, please read Section 6.8 of Chemistry, Blackman et al. (4th ed.) https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 7/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 Naming #2: Cyclic Structures All the prefixes previously introduced can be converted to prefixes for cyclic structures by adding cyclo- to the front. prefix Cyclic version meth- NA eth- NA prop- cycloprop- but- cyclobut- …… …… 1.2 Isomers Isomers are defined as having identical molecular formula but different structure. An isomer cannot convert to another isomer without breaking bonds. There are three main types of isomers in chemistry (The figure below summarises them). This week we introduce: constitutional isomers and diastereoisomers. Constitutional isomers are molecules in which the atoms are connected in different orders. Conformers are not isomers. Instead they are the same chemical structure but have bonds rotated into different 3D structures. Consider the structures shown below. Which are constitutional isomers and which are conformers? NOTE: THE NAMING RULES FOR CONSTITUTIONAL ISOMERS ARE HERE TO HELP YOU APPRECIATE HOW NAMES ARE GENERATED. PLEASE DO NOT MEMORISE THEM. https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 8/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 Naming #3: Constitutional isomer naming Each constitutional isomer is distinguished by name. Their name is derived using three steps. Consider the following structure: Step 1. Identify the longest linear chain and name based on “Naming #1” Step 2. Count from either end of the chain such that the branching point receives the lowest number Step 3. Name the sidegroups at the branching point based on “Naming #1” prefix, but with "-yl" as a suffix. If you have two or more identical sidegroups bonded to the same carbon, you need to add di- (for 2 identical sidegroups) or tri- (for 3 identical sidegroups) before the prefix. In this case we have two methyl groups, so the sidegroup's name is dimethyl Assemble the name in the following order. a) a) Longest linear chain branching point number (i.e. 2); b)-side group name and c) name of longest linear chain. i.e. 2,2-dimethylbutane https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 9/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 1.3. Three-dimensional structure of alkanes Organic molecules are characterised not only by their size (i.e. length of the carbon chain) but also by their shape. Their 3D structure plays a significant role in their physical properties as well as their reactivity. Explore the 3D representation of the molecular structure of ethane illustrated in this ChemTube 3D page (click the link). Using the controls located at the right hand corner of the image of the molecule, explore the different dimensions to get a wider perspective to its shape. https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 10/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 1.4. Alkenes and Alkynes Unsaturated hydrocarbons contain one or more double or triple bonds. Hydrocarbons with double bonds (alkene) have the suffix - ene whereas those hydrocarbons with triple bonds (alkyne) have the suffix -yne. The simplest alkene is ethene, and the simplest alkyne is ethyne. The name is derived from the prefix for 2-carbons (eth-) and the suffix for alkene (-ene) or alkyne (-yne). Alkenes have the general formula C­nH2n. The molecular geometry of a double bond is trigonal planar. Alkynes have the general formula C­nH2n-2. The molecular geometry of a triple bond is linear. 2.1 Alkene Isomers As a result of the restricted rotation about the alkene double bond, isomerism is observed. In this case the isomers are called diastereoisomers. Diastereoisomers have the same connectivity but different positions of groups in space. Consider the example discussed below. 2.2 Naming alkene diastereoisomers Just as we needed a way to name the different constitutional isomers, we need a way to name diastereoisomers. This is achieved by considering the four groups attached to the alkene and assigning a priority to them. The “priority” is simply based on the atomic number. larger atomic number = higher priority. So consider the diastereomeric alkene introduced in section 2.1. First assign priority to the two groups attached to one end of the alkene (step 1). Now consider the other end and do the same thing (step 2). If the “higher” priority groups are on the same side of the alkene then this is called zusammen (Z). If on opposite sides it is called entgegen (E). Zusammen is German for together. Entgegen (E) is German for opposite. https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 11/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 NOTE: YOU NEED TO BE ABLE TO DETERMINE IF AN ALKENE IS "E" OR "Z". BELOW IS AN EXAMPLE OF HOW THIS IS USED TO GENERATE A COMPLETE NAME. THIS SHOULD NOT BE MEMORISED. IT IS JUST FOR INTEREST. Naming #4: Alkenes In section 2.2 we showed how to assign a double bond as E or Z, but how is that used in a name? Consider the structure examined previously introduced. Step 1. Identify the longest linear chain with the alkene in it. Name it using “Naming #1” but change the suffix from –ane to–ene. Step 2. Count from either end of the chain such that the first carbon of the alkene receives the lowest number (e.g. 2 NOT 3 for our example). Step 3. Name any sidegroups based on “Naming #1”, in this case methyl, and assemble the name in the following order. a) Stereochemical designator (E or Z, in italics); b) Branching point (i.e. 4); c)-side group name and d) name of longest linear chain with number for first carbon of alkene embedded (i.e. pent-2-ene). i.e. (E)-4-methylpent-2-ene https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 12/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 Naming #5: Cycloalkenes Cyclic alkenes are named in a similar fashion in two steps. Consider the following example. Step 1. It is a cyclic (cyclo-) five membered (pent-) ring with an alkene (-ene). So from our previous notes on naming it is a cyclopentene. Step 2. Number all carbons in the ring starting from either end of the alkene. The correct numbering gives the lowest number to the substituent. Hence this compound is 3- chlorocyclopentene. https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 13/18 7/26/24, 6:06 PM Week 1: Introduction to Organic Chemistry - workbook | MonashELMS1 2. Summary This week has given you a foundation in organic chemistry, that will be built upon in the following weeks. A key focus of this week has been on understanding the structure and representations of various hydrocarbons. As you have also seen, being able to accurately draw and describe alkanes, alkenes and alkynes is an important skill and is one that you'll have the opportunity to practice more in this unit and your career as chemists. https://learning.monash.edu/mod/book/tool/print/index.php?id=2774224 14/18