Courtney Eichengreen courtney.eichengreen@ucdenver.edu 719.321.4187 Organic Chemistry Courtney Eichengreen courtney.eichengreen@ucdenver.edu 719.321.4187.

Courtney Eichengreen courtney.eichengreen@ucdenver.edu 719.321.4187
Organic Chemistry Courtney Eichengreen 1

Organic Chemistry I From atoms to molecules and beyond Hydrocarbons
Functional Groups Bonding and Molecular Structure Resonance and Isomers Intermolecular interactions Hydrocarbons Substitution and Elimination Reactions Oxygen Containing Compounds Amines 2

Lewis Dot Structures Rules for writing Formal Charge
Find total # valence e- 1 e- pair = 1 bond; Arrange remaining e- per octet rules Except: Period 3 can have expanded octet (vacant d orbital required for hybridization) Formal Charge # valence e- (isolated atom) - # valence e- (lewis structure) Sum of formal charge for each atom is the total charge on the molecule ACTUAL charge distribution depends on electronegativity Expanded octet unpopular 3

Structural Formulas Dash Formula Condensed Formula Bond-line Formula
Fischer projection Newman projection Dash-line-wedge Ball and stick All Images courtesy of Exam Krackers 4

Functional Groups List #1- Critical for the MCAT
Alkane C-C Alkene C=C Alkyne CΞC Alcohol R-OH Ether R-O-R Amine R-N-R2 Aldehyde R-CHO Ketone R2C=O Carboxylic Acid RCOOH Ester RCOOR Amide RCONH2 Atoms  groups 5

Functional Groups List #2- Also Useful
Alkyl Halogen Gem-dihalide Vic dihalide Hydroxyl Alkoxy Hemiacetal Hemiketal Mesyl group Tosyl group Carbonyl Acetal Acyl Anhydride Aryl Benzyl Phenyl Hydrazine Hydrazone Vinyl Vinylic Allyl Nitrile Epoxide Enamine Imine Nitro Nitroso Learn bolded groups 6

For your reference 7

Bonds Types: Ionic Covalent Polar covalent Hydrogen Bonds
Coordinate covalent Polar covalent Hydrogen Bonds complete transfer of electrons shared electrons One atom provides both electrons in a shared pair. unequal sharing of electrons bonds between polar molecules containing H and O, N, or F Atoms  groups  molecules 8

Covalent Bonds Sigma s Pi P Between s orbitals
Small, strong, lots of rotation Pi P Between p orbitals Discreet structure, weaker than sigma, no rotation 9

Covalent Bonds 10

Bonds In the pi bond of an alkene, the electron pair have:
33% p character and are at a lower energy level than the electron pair in the s bond. 33% p character and are at a higher energy level than the electron pair in the s bond. 100% p character and are at a lower energy level than the electron pair in the s bond. 100% p character and are at a higher energy level than the electron pair in the s bond. Higher energy because of node – see previous image. Pi bonds more strained in space, less stable  higher energy 11

Hybridization In order for electrons to be “available” for bonding, they have to physically spread out in space = hybridization of orbitals into “sp” rather than purely p or purely s 12

Hybridization Remember: All pi bonds are between P orbitals
“Leftover” P and S orbitals hybridize, participate in sigma bonds Ex: H2C=CH2

Hybrid Bonds -ane -ene -yne -yl Suffix C bonds Hybridization Percent
S:P Bond Angle Bond Length Bond Strength -ane -ene -yne -yl 14

Hybrid Bonds Percent S:P -ane C-C sp3 25:75 109.5 154 346 -ene C=C sp2
Suffix C bonds Hybridization Percent S:P Bond Angleo Bond Length (pm) Bond Strength (kJ/mol) -ane C-C sp3 25:75 109.5 154 346 -ene C=C sp2 33:66 120 134 612 -yne sp 50:50 180 835 -yl Side chain Individual pi bonds are weaker, but pi + sigma is stronger than sigma alone! Notice ratio of changes, C=C is NOT twice C-C

Special Cases – O and N Know typical bonding for C, N, O
Bond angles in N compounds Lone pair occupies more space than sigma bond Bond angles 107.3 Bond angles in O compounds Bond angles 104.5 Know typical bonding for C (4) , N (3+LP), O (2+2LP) In compounds with LPs – bond angles COMPRESSED Will be asked to rank bond angles not know exact numbers  16

For the molecule 1,4 pentadiene, what type of hybridization is present in carbons # 1 and # 3 respectively? A) sp2, sp2 B) sp2, sp3 C) sp3, sp3 D) sp3, sp2 17

VSEPR: molecular geometry
valance shell electron pair repulsion GEOMETRY = Minimize electron repulsion Draw the Lewis dot structure. Place electron pairs as far apart as possible, then large atoms, then small atoms. Name the molecular structure based on the position of the atoms 18

Trigonal bipyramidal, dsp3
VSEPR 1. Draw the Lewis dot structure 2. Place electron pairs as far apart as possible then large atoms, then small atoms 3. Name the molecular structure based on the position of the atoms molecule Lewis structure Shape BeCl2 Linear, sp SF4 Seesaw SO3 Trigonal planar, sp2 ICl3 T shaped NO2- Bent CH4 Tetrahedral, sp3 NH3 Trigonal Pyramidal PCl5 Trigonal bipyramidal, dsp3 SF6 Octahedral, d2sp3 IF5 Square Pyramidal ICl4- Square Planar Know bolded geometries! 19

NOW LET’S MOVE STUFF AROUND!
We’ve seen static properties of atoms and molecules… Atoms – formal charge, functional groups Molecules – bonding and geometry Next: comparing different molecules – resonance and isomerism NOW LET’S MOVE STUFF AROUND!

Delocalized e- and Resonance
Resonance forms differ only in location of e- To be a significant resonance form, must be stable Remember octet rule, and consider formal charge Real structure = blend of possible resonance structures, “resonance hybrid” Why does this matter? … (Passage 25) 21

Resonance: Acids and Bases
Conjugate stabilized by RESONANCE Organic Acids- Presence of positively charged H+ present on a OH such as methyl alcohol present on a C next to a C=O such as acetone (alpha C) Organic Bases- Presence of lone pair e to bond to H Nitrogen containing molecules are most common Oxygen containing molecules can act as bases w strong acids Lewis definition – important in OChem because conjugate often stabilized by resonance 22

Stereochemistry Isomers: same molecular formula, different spatial arrangements Different spatial arrangements  different physical and chemical properties! 23

Stereochemistry: Isomers
CONNECTIVITY Structural (constitutional) isomers: Different connectivity. C4H10 - Isobutane vs n-butane Same connectivity, different spatial arrangement: Stereoisomers

ROTATION Conformational isomers: Different spatial arrangement of same molecule, but doesn’t require bond breaking to interconvert! “rotational” isomers Chair vs. boat, Staggered vs Eclipsed, Gauche vs Anti DOES require bond breaking to interconvert: configurational isomers

DOUBLE BOND Geometric isomers: differ in arrangement about a double bond Cis vs. trans Stereoisomers that are not rotational and have no double bond: OPTICAL isomers

CHIRAL ARRANGEMENT Enantiomers: non-superimposable mirror images Same physical properties (MP, BP, density, solubility, etc.) except rotation of light and reactions with other chiral compounds Chiral centers that are all opposite each other (R/S) Diastereomers: chiral molecules with other than exactly opposite stereocenters (not mirror images) 27

What kind of isomers are the two compounds below? A. Diastereomers B. Enantiomers C. Constitutional isomers D. Geometric Isomers 28

Stereochemistry: Rotating Light
Enantiomers differ in rotation of plane-polarized light Excess of one enantiomer causes rotation: Right, clockwise, dextrarotary (d), or + Left, counterclockwise, levarotary (l), or – Specific rotation [a] = a / (l*d) Racemic: 50:50 mixt of enantiomers, NO net rotation Same as R and S? NO Meso molecule – NO net rotation, internal symmetry Normalize rotation for L = path length, d = density. Think of specific gravity, density/density of water +/- = relative configuration, NOT absolute What other compounds with chiral centers have no net rotation of pp light? Meso compounds! 29

Stereochemistry: Chirality
R and S: 1. Assign priority by atomic number If attachments are the same, look at the b atoms 2. Orient lowest priority (#4) away from the observer 3. Draw a circular arrow from 1 to 2 to 3 R = clockwise S = counterclockwise E and Z: Different than cis and trans Z= same side of high priority groups E=opposite side of high priority groups Meso compounds: internal symmetry (passage 27) 30

WHAT ABOUT BETWEEN MOLECULES?
Now we know everything about what happens WITHIN molecules… Then we’ll take a break  WHAT ABOUT BETWEEN MOLECULES?

Intermolecular interactions
Due to DIPOLE MOMENTS Charge distribution of bond is unequal Molecule with dipole moment = polar Molecule without dipole moment = nonpolar Possible to have nonpolar molecules with polar bonds Induced Dipoles Spontaneous dipole moment in nonpolar molecule Occurs via: polar molecule, ion, or electric field Instantaneous Dipole Due to random e- movement (just a quick aside)

Intermolecular interactions
London Dispersion Forces Between 2 instantaneous dipoles Dipole-dipole interactions Dipole-dipole or dipole-induced dipole Hydrogen Bonds Strongest dipole-dipole interaction London Dispersion Forces Between 2 instantaneous dipoles Responsible for phase change of nonpolar molecules Dipole-dipole interactions Dipole-dipole or dipole-induced dipole Hydrogen Bonds Strongest dipole-dipole interaction Responsible for high BP of water

When albuterol is dissolved in water, which of the following hydrogen-bonded structures does NOT contribute to its water solubility? That’s all we’re going to do on intermolecular interactions for now – remember you will need to apply Gen Chem concepts to Ochem problems on Test Day! 34

The first and simplest class of molecules we need to get friendly with for Test Day:
HYDROCARBONS

IUPAC Naming Conventions
IUPAC Rules for Alkane Nomenclature 1. Find + name the longest continuous carbon chain. 2. Identify and name groups attached to this chain. 3. Number the chain consecutively, starting at the end nearest highest priority (oxidation) substituent group. 4. Name the compound listing groups in alphabetical order, preceded by their number in the compound. (di, tri, tetra etc., don’t count for alphabetizing). MCAT secret: on Test Day, you’ll only ever have to MATCH to the correct name! 36

Hydrocarbons # of C Root Name 1 meth 6 hex 2 eth 7 hept 3 prop 8 oct 4
but 9 non 5 pent 10 dec KNOW THESE 37

Hydrocarbons Saturated: CnH(2n+2)
Unsaturated: one or more pi bonds; each pi bond decreases # of H by 2 Primary, secondary, tertiary, and quaternary carbons Know and be able to recognize the following structures n-propyl Iso-propyl n-butyl sec-butyl iso-butyl tert-butyl 38

Alkanes Physical Properties:
Straight chains: MP and BP increase with length Branched chains: BP decreases (less surface area,  vDW forces) MP – a little more complicated due to crystal structure When compared to the straight chain analog, the straight chain will have a higher MP than the branched molecule. BUT, amongst branched molecules, the greater the branching, the higher the MP. C1-4: gas C5-17: liquid C18+: solid (Straight chain) 39

Alkanes-Important Reactions Pretty Darn Unreactive
Combustion: Alkane + Oxygen + High energy input (fire) Products: H2O, CO2, Heat Halogenation Initiation with UV light Homolytic cleavage of diatomic halogen Yields a free radical Propagation (chain reaction mechanisms) Halogen radical removes H from alkyl Yields an alkyl radical, which can make more radicals Termination Radical bonds to another radical Reactivity of halogens: F > Cl > Br >>> I Selectivity of halogens (How selective is the halogen in choosing a position on an alkane): I > Br > Cl > F more electronegative means less selective Stability of free radicals: more substituted = more stable, so most sub’d C aryl>>>alkene> 3o > 2o > 1o >methyl 40

Cycloalkanes General formula: (CH2)n or CnH2n
Nomenclature: It’s the same! As MW increases BP increases; MP fluctuates (crystal stacking with different geometry) Ring strain in cyclic compounds: Zero for cyclohexane (All C-C-C bond angles: 111.5°) Increases as rings become smaller or larger (up to cyclononane) 41

Cycloalkanes Cyclohexane Exist as “chair” and “boat” conformations
Chair conformation preferred because it is at the lowest energy. (WHY?) Substituents can occupy axial and equatorial positions. Axia (6) - perpendicular to the ring Equatorial (6)- roughly in the plane of the ring Big substituents prefer to be equatorial – less “crowding”! When the ring reverses its conformation, substituents reverse their relative position Chair conformation preferred because it is at the lowest energy. WHY? – bonds staggered not eclipsed! By “crowding” I mean nonbonded strain. 42

Cyclohexanes In a sample of cis-1,2-dimethylcyclohexane at room temperature, the methyl groups will: Both be equatorial whenever the molecule is in the chair conformation. Both be axial whenever the molecule is in the chair conformation. Alternate between both equatorial and both axial whenever the molecule is in the chair conformation Both alternate between equatorial and axial but will never exist both axial or both equatorial at the same time 43

Things start getting more exciting once we start substituting H for more interesting functional groups… so let’s get ready for some These apply to halogen-containing, oxygen-containing, nitrogen-containing compounds etc. Next time we’ll look at specific unique properties of O and N compounds REACTIONS!!

Substitutions Substitution: one functional group replaces another
Electrophile: wants electrons, has partial + charge Nucleophile: donates electrons, has partial – charge Familiarize yourself with these common nucleophiles (may be in solution as conjugate acid, or salt) (salt just means ionic compound!) 45

Eliminations Elimination: functional group lost, double bond made
Often, a Lewis base is responsible for taking H leaving behind an extra pair of e- for the = The opposite of elimination is addition 46

Substitution and Elimination
SN1: substitution, nucleophilic, unimolecular Mechanism: two-step 1. spontaneous formation of carbocation (SLOW) 2. Nucleophile attacks carbocation Kinetics: rate depends only on the substrate, R=k[reactant] Stereochemistry: racemization of chiral substrates Favored with weak or bulky Nu, good LG, stable carbocation Protic solvents stabilize carbocation Can see carbocation rearrangement Chiral reactants  racemic product mixture 47

E1: elimination, unimolecular Mechanism: two-step 1. spontaneous formation of carbocation (SLOW) 2. Base abstracts beta H Kinetics: rate depends only on the substrate, R=k[reactant] Favored with good LG, stable carbocation, weak base Protic solvents stabilize carbocation Can see carbocation rearrangement 48

Which of the following carbocations is the most stable?
CH3CH2CH2CH2 B. CH3CH2CH2CHCH3 C. (CH3)3C D. CH3 49

SN2: substitution, nucleophilic, bimolecular Mechanism: CONCERTED Kinetics: rate depends on substrate+nucleophile, R=k[Nu][E] Stereochemistry: inversion of configuration (but watch your R and S!) Favored with poor LG, small + strong Nu Polar, APROTIC solvents don’t obstruct Nu 50

E2: elimination, bimolecular Mechanism: CONCERTED Anti-peri-planar transition state determines stereochemistry Kinetics: rate depends on substrate+base, R=k[substrate][B] Favored with strong bulky base If you see HEAT, think Elimination E2 reactions often run in solvent of conjugate acid (WHY?) “Anti” = sterics, “periplanar” = same plane. To make a new double bond, e- flow in aligned pi system. Run in solvent of conjugate acid so there’s nobody else for the strong base to react with! 51

Benzene A special molecule, a special case of substitution!
Actually, it’s addition and then elimination. Aromatic molecule, Stabilized by resonance Undergoes net substitution not addition (WHY?) Substituents determine subsequent reactivity: Electron donating groups activate the ring and are ortho-para directors Electron withdrawing groups deactivate the ring and are meta directors Halogens are electron withdrawing BUT are ortho-para directors Aromaticity: huckel’s rule (4n+2 pi electrons), cyclic, planar, conjugated Addition would result in a not-aromatic product – very unstable, relative to benzene! 52

Benzene: Substituent Effects
53

In what order were the substituents added? How can you tell?
Oh activating but OP directing!! No2 meta directing

OXYGEN-CONTAINING COMPOUNDS
Another class of molecules we need to be familiar with: OXYGEN-CONTAINING COMPOUNDS

Oxygen Containing Compounds
Alcohols Aldehydes and Ketones Carboxylic Acids Acid Derivatives Acid Chlorides Anhydrides Amides Keto Acids and Esters 56

Alcohols One of the most common reactions of alcohols is nucleophilic substitution. Which of the following are TRUE in regards to SN2 reactions: Inversion of configuration occurs Racemic mixture of products results Reaction rate = k [S][nucleophile] I only II only I and III only I, II, and III 57

Alcohols Physical Properties: General principles Polar
High MP and BP (WHY?) More substituted = less acidic (CH3)3COH: pKa = 18.00 CH3CH2OH: pKa = 16.00 CH3OH: pKa = 15.54 Electron withdrawing substituents stabilize alkoxide ion and lower pKa. Tert-butyl alcohol: pKa = 18.00 Nonafluoro-tert-butyl alcohol: pKa = 5.4 General principles H bonding Acidity: weak relative to other O containing compounds (CH groups are e- donating = destabilize deprotonated species) 58

Alcohols Naming Select longest C chain containing the hydroxyl group and derive the parent name by replacing –e ending of the corresponding alkane with –ol. Number the chain beginning at the end nearest the –OH group. Number the substituents according to their position on the chain, and write the name listing the substituents in alphabetical order. 59

Alcohols-Oxidation & Reduction
60 Reduction

Alcohols-Oxidation & Reduction
Common oxidizing and reducing agents Generally for the MCAT Oxidizing agents have lots of oxygens Reducing agents have lots of hydrogens Oxidizing Agents Reducing Agents K2Cr2O7 LiAlH4 KMnO4 NaBH4 H2CrO4 H2 + Pressure O2 Br2 61

Making Alcohols: reduction synthesis
Aldehydes, ketones, esters, and acetates can be reduced to alcohols w strong reducing agents such as NaBH4 and LiAlH4 Electron donating groups increase the negative charge on the carbon and make it less susceptible to nucleophilic attack. Reactivity: Aldehydes>Ketones>Esters/acetates Only LiAlH4 is strong enough to reduce esters and acetates 62

Alcohols to Alkylhalides via a strong acid catalyst
R-OH + HCl  RCl + H20 -OH is converted to a much better leaving group when protonated by a strong acid For tertiary alcohols: HCl or HBr Primary/secondary alcohols are harder, need SOCl2 or PBr3 63

In the reaction above, if the reagents in the first step were replaced with LiAlH4, what product would result? a) c) b) d) O OH OH OH OH OH OH HO 64

Carbonyls Carbon double bonded to Oxygen
Planar stereochemistry Partial positive charge on Carbon (susceptibility to nucleophilic attack) Aldehydes & Ketones (nucleophilic addition) Carboxylic Acids (nucleophilic substitution) Amides All carbonyls – the basic reaction 65

Aldehydes and Ketones Physical properties: General principles:
Carbonyl group is polar Higher BP and MP than alkanes (WHY?) More water soluble than alkanes (WHY?) Trigonal planar geometry, reduction yields racemic mixtures General principles: Effects of substituents on reactivity of C=O: e- withdrawing increase the carbocation nature and make the C=O more reactive Steric hindrance: ketones are less reactive than aldehydes Acidity of alpha hydrogen: carbanions a, b unsaturated carbonyls: resonance structures 66

Aldehydes and Ketones Naming – lalala it’s the same rules!
Naming Aldehydes Replace terminal –e of corresponding alkane with –al. Parent chain must contain the –CHO group The –CHO carbon is C1 When –CHO is attached to a ring, we say “carbaldehyde” Naming Ketones Replace terminal –e of corresponding alkane with –one. Parent chain is longest chain containing ketone Numbering begins at the end nearest the carbonyl C. 67

Aldehydes and Ketones- Acetal and Ketal Formation nucleophilic addition at C=O bond
68

Aldehydes and Ketones Keto-enol Tautomerism:
Keto tautomer is preferred (alcohols are more acidic than aldehydes and ketones). 69

Guanine, the base portion of guanosine, exists as an equilibrium mixture of the keto and enol forms. Which of the following structures represents the enol form of guanine? 70

Aldehydes and Ketones-reactions at adjacent positions
Aldol (aldehyde + alcohol) condensation: Occurs at the alpha carbon Pi electrons in enol act as nucleophile Base catalyzed condensation (removal of H2O) Can use mixtures of different aldehydes and ketones 71

Aldehydes and Ketones-Oxidation (Aldehydes  Carboxylic acids)
Aldehydes are easy to oxidize because of the adjacent hydrogen. In other words, they are good reducing agents. Examples used as indicators: Potassium dichromate (VI): orange to green Tollens’ reagent (silver mirror test): grey ppt. Fehlings or benedicts solution (copper solution): blue to red Ketones (no adjacent H) are resistant to oxidation. 72

Aldehydes and Ketones Organometallic reagents:
Nucleophilic addition of a carbanion to an aldehyde or ketone to yield an alcohol Organometallic just means carbanion 73

Carboxylic Acids General Principles:
Electrophilic carbonyl C susceptible to nucleophilic attack! Fairly strong acids (compared to other organic Oxygen containing compounds) Acidity of terminal H increases with EWG, decreases with EDG – always consider stability of conjugate base Planar, polar, H bonding 74

Which class of compounds would have a higher boiling point, Acyl Chlorides or Carboxylic Acids? Why?
No H bonding in acyl chloride, RC=OCl

Carboxylic Acids Naming
Carboxylic acids derived from open chain alkanes are systematically named by replacing the terminal –e of the corresponding alkane name with –oic acid. Compounds that have a –CO2H group bonded to a ring are named using the suffix –carboxylic acid. The –CO2H group is attached to C #1 and is not itself numbered in the system. 76

Carboxylic Acids-important reactions
Carboxyl group reactions: Nucleophilic attack: Carboxyl groups and their derivatives undergo nucleophilic substitution. Aldehydes and Ketones undergo addition (WHY?) Must contain a good leaving group or a substituent that can be converted to a good leaving group. because they lack a good leaving group. 77

Reduction: Form a primary alcohol LiAlH4 is the reducing agent LiAlH4 CH3(CH2)6COOH CH3(CH2)6CH2OH 78

Carboxyl group reactions: Decarboxylation: know that it happens (-CO2) 79

Fischer Esterification Reaction: Alcohol + Carboxylic Acid  Ester + Water Acid Catalyzed- protonates –OH to H2O (excellent leaving group) Alcohol performs nucleophilic attack on carbonyl carbon H+ These bonds are broken 80

Carboxylic Acids- reactions at two positions
Substitution reactions: keto reactions shown, consider enol reactions To make -> SOCl2 or PCl3 Heat, -H2O R'OH, heat, H+ - R2NH heat HO- 81

Carboxylic Acids- reactions at two positions
Halogenation: enol tautomer undergoes halogenation 82

Acid Derivatives Naming
Acid Halides (RCOX) “-oyl halide” instead of “-oic acid” ex: ethanoyl chloride Acid Anhydrides (RCO2COR’) Just replace the word acid with anhydride. 2 acetic acid  acetic anhydride Unsymmetrical anhydrides are named by citing the two acids alphabetically. Acetic acid + benzoic acid  acetic benzoic anhydride Esters (RCO2R’) Name R’ (on the –O– side) with “-yl”, R (on the =O side) with “-oate” ex: isopropyl propanoate Amides (RCONH2) Just use the suffix “amide” Acetic acid  acetamide If the Nis further substituted, first identify the substituent groups and then the parent amide. The substituents are preceded by the letter N. Propanoic acid + methyl amine  N-Methylpropanamide 83

Acid Derivatives- Relative Reactivity
A more reactive acid derivative can be converted to a less reactive one, but not vice versa Only esters and amides commonly found in nature. Acid halides and anhydrides react rapidly with water and do not exist in living organisms 84

Acid Derivatives- Reactions of Derivatives
Hydrolysis- +water  carboxylic acid Alcoholysis- +alcohol  ester Aminolysis- +ammonia or amine  amide Reduction- + H-  aldehyde or alcohol Grignard- + Organometallic  ketone or alcohol 86

Acid Derivatives Transesterification
Transesterification: exchange alkoxyl group with ester of another alcohol Alcohol + Ester  Different Alcohol + Different Ester (passage 26) 87

Courtney Eichengreen courtney.eichengreen@ucdenver.edu 719.321.4187 Organic Chemistry Courtney Eichengreen courtney.eichengreen@ucdenver.edu 719.321.4187.

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