Chapter 1:Organic Chemistry ll:Here We Go Again! 11 as Na',or anions,such as Cl.Cations may include an ammonium ion from an amino group,such as RNH,'.The anion may be from a carboxylic acid,such as RCOO-.The oppositely charged ions attract each other very strongly. Functional groups nany different e f tional a n and/or double or triple In Organic I you probably started with the hydrocarbons,compounds of carbon and hydrogen,including the alkenes and alkynes that contained double and single bonds,respectively.Then you probably touched on some of the more common functional groups,such as alcohols and maybe even some aromatic compounds. Reactions You encountered a lot of reactions in Organic I.Every time you encountered a different functional group,you had a slew of reactions to learn.Reactions that told how the functional group could be formed,common reactions that the functional group underwent-reactions,reactions,and more reactions. hope you learned them well,because e seeing them again quite often Spectroscopy In OrganicI you probably learned a lot about the different types of spectroscopy and how they're used in structure determina covered how mass ve yo an 554 ragments may be pre th molecule b onal groups,an on.The y00 nce ols of h splittin ns to you clues about structure
Chapter 1: Organic Chemistry II: Here We Go Again! 11 In organic reactions, ionic interactions may serve as intermolecular or intramolecular forces. In some cases, these may involve metal cations, such as Na+, or anions, such as Cl– . Cations may include an ammonium ion from an amino group, such as RNH3 +. The anion may be from a carboxylic acid, such as RCOO– . The oppositely charged ions attract each other very strongly. Functional groups Carbon is an extremely versatile element because it can form many different compounds. Most of the compounds have one or more functional groups, which contain atoms other than carbon and hydrogen and/or double or triple bonds, and define the reactivity of the organic molecule. In Organic I you probably started with the hydrocarbons, compounds of carbon and hydrogen, including the alkenes and alkynes that contained double and single bonds, respectively. Then you probably touched on some of the more common functional groups, such as alcohols and maybe even some aromatic compounds. Reactions You encountered a lot of reactions in Organic I. Every time you encountered a different functional group, you had a slew of reactions to learn. Reactions that told how the functional group could be formed, common reactions that the functional group underwent — reactions, reactions, and more reactions. Two of the most important ones you learned were substitution and elimination reactions: SN1, SN2, E1, and E2. We hope you learned them well, because you’ll be seeing them again quite often. Spectroscopy In Organic I you probably learned a lot about the different types of spectroscopy and how they’re used in structure determinations. You discovered how mass spectroscopy can give you an idea about molar mass and what fragments may be present in the molecule. You found out that infrared spectroscopy can be used to identify functional groups, and you learned to look at the fingerprint region. Then finally you progressed to nuclear magnetic resonance (NMR) spectroscopy, one of the main tools of organic chemists, which can be used to interpret chemical shifts and splitting patterns to give you more clues about structure. 05_178157-ch01.indd 11 5/28/10 9:45 AM
12 Part l:Brushing Up on Important Organic Chemistry I Concepts Isomerism and optical activity During organic i you were exposed to the concepts associated with isomerism and optical activity.You need to be familiar with these concepts in Organic lI,so we take a few minutes here for a brief review. somers are compounds with the same molecular formula but different structural formulas.Some organic and biochemical compounds may exist in different isomeric forms,and these different isomers have different properties. The two most common types of isomers in organic isomers and isomerism due to the presence of a chiral carbon Cis-trans isomers The presence of carbon-carbon double bonds leads to the possibility of isomers.Do ble bonds are rather restrictive and limit molecular movement Groups on the same side of the d ouble bond tend to remain i hat position hch other (rns group o rem across th e 1 ever of fatty acids.but pro nds to convert some of the cis isom ers to the trans isomers. Figure 1-1 trans C some Cis isomer Trans isomer Cis-trans isomers are also possible in cyclic systems.The cis form has similar groups on the same side of the ring,while the trans form has similar groups above and below the ring. Chiral compounds A carbon atom with four different groups attached is chiral.A chiral carbon e waves are al in the e same pla e,anc nas an end me (non-supermpo or image).Rotati ich may eithe the righ (de one optical isomer eing d al
12 Part I: Brushing Up on Important Organic Chemistry I Concepts Isomerism and optical activity During Organic I you were exposed to the concepts associated with isomerism and optical activity. You need to be familiar with these concepts in Organic II, so we take a few minutes here for a brief review. Isomers are compounds with the same molecular formula but different structural formulas. Some organic and biochemical compounds may exist in different isomeric forms, and these different isomers have different properties. The two most common types of isomers in organic systems are cis-trans isomers and isomerism due to the presence of a chiral carbon. Cis-trans isomers The presence of carbon-carbon double bonds leads to the possibility of isomers. Double bonds are rather restrictive and limit molecular movement. Groups on the same side of the double bond tend to remain in that position (cis), while groups on opposite sides tend to remain across the bond from each other (trans). You can see an example of each in Figure 1-1. However, if the two groups attached to either of the carbon atoms of the double bond are the same, cis-trans isomers are not possible. Cis isomers are the normal form of fatty acids, but processing tends to convert some of the cis isomers to the trans isomers. Figure 1-1: Cis and trans isomers. Cis isomer Trans isomer H Cl Cl H C C H C C Cl H Cl Cis-trans isomers are also possible in cyclic systems. The cis form has similar groups on the same side of the ring, while the trans form has similar groups above and below the ring. Chiral compounds A carbon atom with four different groups attached is chiral. A chiral carbon rotates plane-polarized light, light whose waves are all in the same plane, and has an enantiomer (non-superimposable mirror image). Rotation, which may be either to the right (dextrorotatory) or to the left (levorotatory), leads to one optical isomer being d and the other being l. Specific rotation (represented 05_178157-ch01.indd 12 5/28/10 9:45 AM
Chapter 1:Organic Chemistry ll:Here We Go Again 13 by [al.where a=observed rotation,T=temperature,and D=sodium D line) is a measure of the ability of a compound to rotate light.The specific rotation comes from the observed rotation (a)divided by the product of the concen- tration of the solution and the length of the container.Other than optical activity,the physical properties of enantiomers are the same. A racemic mixture is a 50:50 mixture of the enantiomers A meso compound is aco mpound with chiral centers and a pl The plane cance gheopteaYoeaiaotsom Diastereomers are stereoisomers that aren't enantiomers. R-S notation is a means of designating the geometry around the chiral center This method rec uires the grouns attached to the chiral center to he priori. tized in order of decreasing atomic weight.To assign the center,place the lowest priority group (the group with the lowest atomic weight)on the far side and count the remaining groups as 1,2,and 3.Counting to the right is R and counting to the left is S.Any similarity between d and and R and S is coincidental. Some important organic compounds have more tha one chiral center stereo mers ster e number of non enter 1-2 ows the ur ste A present i a mol ror hile the the enantion iaste diffe ent physical properti CHOH Figure 1-2: Representa- tionsofa molecule with twc nantiome chira centers Diastereomers
Chapter 1: Organic Chemistry II: Here We Go Again! 13 by [α] T D , where α = observed rotation, T = temperature, and D = sodium D line) is a measure of the ability of a compound to rotate light. The specific rotation comes from the observed rotation (α) divided by the product of the concentration of the solution and the length of the container. Other than optical activity, the physical properties of enantiomers are the same. A racemic mixture is a 50:50 mixture of the enantiomers. A meso compound is a compound with chiral centers and a plane of symmetry. The plane of symmetry leads to the optical rotation of one chiral carbon cancelling the optical rotation of another. Diastereomers are stereoisomers that aren’t enantiomers. R-S notation is a means of designating the geometry around the chiral center. This method requires the groups attached to the chiral center to be prioritized in order of decreasing atomic weight. To assign the center, place the lowest priority group (the group with the lowest atomic weight) on the far side and count the remaining groups as 1, 2, and 3. Counting to the right is R and counting to the left is S. Any similarity between d and l and R and S is coincidental. Some important organic compounds have more than one chiral center. Multiple chiral centers indicate the presence of multiple stereoisomers. The maximum number of stereoisomers is 2n where n is the number of nonidentical chiral centers. Figure 1-2 shows the four stereoisomers present in a molecule with two chiral centers. Non-superimposable mirror images are enantiomers, while the other species in the figure are diastereomers. Unlike enantiomers, diastereomers have different physical properties. Figure 1-2: Representations of a molecule with two chiral centers. CH H OH OH HO HO H H * * * * CH2OH H O Enantiomers Diastereomers C C CH HO H O * * CH2OH H O C C C CH2OH O H C C H HO OH H * * C CH2OH O H C C Enantiomers 05_178157-ch01.indd 13 5/28/10 9:45 AM
14 Part l:Brushing Up on Important Organic Chemistry I Concepts Emil Fischer developed a method of drawing a compound to illustrate which stereoisomer is present.Drawings of this type,called Fischer projection formulas are very useful in biochemistry.In a projection formula,a chiral carbon is placed in the center of a pattern.The vertical lines (bonds)point away from the viewer,and the horizontal lines point towards the viewer.Fischer CHO CHO Figure 1-3: -OH H01 CH2OH CH,OH D-glyceraldehyde L-glyceraldehyde The use of D and L is gradually being replaced by the R and Ssystem of ricriyre hone chral Looking Ahead to Organic Chemistry 1] One of the keys to Organic lI is mechanisms,the specific way in which a reaction proceeds.Recall from Organic I that this involves pushing around electrons,showing where they're going with curved arrows.We give you a good review of these concepts in Chapter 2,along with some basic reaction moves. when we encounter a new I ns.In some courses and st se tho en't gotte this out le with that I free to skip that chapter and go on
14 Part I: Brushing Up on Important Organic Chemistry I Concepts Emil Fischer developed a method of drawing a compound to illustrate which stereoisomer is present. Drawings of this type, called Fischer projection formulas, are very useful in biochemistry. In a projection formula, a chiral carbon is placed in the center of a + pattern. The vertical lines (bonds) point away from the viewer, and the horizontal lines point towards the viewer. Fischer used the D designation if the most important group was to the right of the carbon, and the L designation if the most important group was to the left of the carbon. (See Figure 1-3.) Figure 1-3: The Fischer projection formulas. H H C C OH HO CHO CHO D-glyceraldehyde L-glyceraldehyde CH2OH CH2OH The use of D and L is gradually being replaced by the R and S system of designating isomers, which is particularly useful when more than one chiral carbon atom is present. Looking Ahead to Organic Chemistry II One of the keys to Organic II is mechanisms, the specific way in which a reaction proceeds. Recall from Organic I that this involves pushing around electrons, showing where they’re going with curved arrows. We give you a good review of these concepts in Chapter 2, along with some basic reaction moves. In Chapter 3 we go into some depth about alcohols and ethers. Like Organic I, when we encounter a new functional group we examine the structure, nomenclature, properties, synthesis, and reactions. In some courses and textbooks, alcohols are covered in the first semester, but for those readers who haven’t gotten to them yet, we include them in this book. If you’re already comfortable with that material, please feel free to skip that chapter and go on to another. 05_178157-ch01.indd 14 5/28/10 9:45 AM
Chapter 1:Organic Chemistry ll:Here We Go Again 15 Conjugated unsaturated systems spend a little time ortant part of org o ab thos stems.setting the stage for our discussion of aromatic compo unds that you can find in Chapter 6. To bring you up to speed on spectroscopy,we cover the basics in Chapter 5. We give you the executive summary on infrared (IR).ultraviolet-visible (UV-vis),mass spectrometry (mass spec),and nuclear magnetic resonance (NMR).In addition,many of the chapters in this book have a spectroscopy section at the end where we simply cover the essentials concerning the specific compounds that you study in that chapter. Aromatic nds and their reactions are abig part of any Organic ll course.We introdu ce you to the aromatic family.in ding the he ou may w. on the cept of resonance out more than y about aromatic sub stitution reactions,starring electrophiles Another important part of Organic Il is carbonyl chemistry.We look at the basics of the carbonyls in Chapter 9.It's like a family reunion where I (John. one of your authors)grew up in North Carolina- everybody is related You meet aldehydes,ketones,carboxylic acids,acyl chlorides,esters,amides,and on and on.It's a quick peek,because later we go back and examine many of these in detail.For example,in Chapter 10 you study aldehydes and ketones. along with some of the amines,while in Chapter 11 we introduce you to other carbonyl compounds,enols and enolates,along with nitroalkanes and nitriles. ives are also an important part of Organic ing at structure, ature sp rboxyli Whi this 10 acids we u hen yo ry ch co or quick review or Du tte d by Wiley.) Carbon compounds that also contain nitrogen,such as the amines,play a significant part of any Organic ll course.You encounter more acid-base chemistry with the amines.along with some more reactions.We hit this topic in Chapter 13 and give you some tips for multistep synthesis. You probably haven't considered the fact that some organic compounds may contain a metal,so we give you an opportunity to become familiar with the organometallics in Chapter 14.In this chapter you meet the Grignard reaction. It's a very important organic reaction that you may have the opportunity to run in organic lab
Chapter 1: Organic Chemistry II: Here We Go Again! 15 Conjugated unsaturated systems are an important part of organic chemistry, so in Chapter 4 we spend a little time talking about those systems, setting the stage for our discussion of aromatic compounds that you can find in Chapter 6. To bring you up to speed on spectroscopy, we cover the basics in Chapter 5. We give you the executive summary on infrared (IR), ultraviolet-visible (UV-vis), mass spectrometry (mass spec), and nuclear magnetic resonance (NMR). In addition, many of the chapters in this book have a spectroscopy section at the end where we simply cover the essentials concerning the specific compounds that you study in that chapter. Aromatic compounds and their reactions are a big part of any Organic II course. We introduce you to the aromatic family, including the heterocyclic branch, in Chapter 6. (You may want to brush up on the concept of resonance beforehand.) Then in Chapters 7 and 8, you find out more than you ever wanted to know about aromatic substitution reactions, starring electrophiles and nucleophiles. Another important part of Organic II is carbonyl chemistry. We look at the basics of the carbonyls in Chapter 9. It’s like a family reunion where I (John, one of your authors) grew up in North Carolina — everybody is related. You meet aldehydes, ketones, carboxylic acids, acyl chlorides, esters, amides, and on and on. It’s a quick peek, because later we go back and examine many of these in detail. For example, in Chapter 10 you study aldehydes and ketones, along with some of the amines, while in Chapter 11 we introduce you to other carbonyl compounds, enols and enolates, along with nitroalkanes and nitriles. Carboxylic acids and their derivatives are also an important part of Organic II. We spend quite a few pages looking at the structure, nomenclature, synthesis, reactions, and spectroscopy of carboxylic acids. While on this topic in Chapter 12, we use a lot of acid-base chemistry, most of which you were exposed to in your introductory chemistry course. (For a quick review, look over a copy of Chemistry For Dummies or Chemistry Essentials For Dummies, both written by John T. Moore and published by Wiley.) Carbon compounds that also contain nitrogen, such as the amines, play a significant part of any Organic II course. You encounter more acid-base chemistry with the amines, along with some more reactions. We hit this topic in Chapter 13 and give you some tips for multistep synthesis. You probably haven’t considered the fact that some organic compounds may contain a metal, so we give you an opportunity to become familiar with the organometallics in Chapter 14. In this chapter you meet the Grignard reaction. It’s a very important organic reaction that you may have the opportunity to run in organic lab. 05_178157-ch01.indd 15 5/28/10 9:45 AM