Organic Chemistry
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Transcript of Organic Chemistry
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Organic Chemistry I
From atoms to molecules and beyond Functional Groups Bonding and Molecular Structure Resonance and Isomers Intermolecular interactions
Hydrocarbons Substitution and Elimination Reactions Oxygen Containing Compounds Amines
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Lewis Dot Structures
Rules for writing 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
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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
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Functional GroupsList #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
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Functional GroupsList #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
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Bonds
Types: Ionic
Covalent 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
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Covalent Bonds Sigma
Between s orbitals Small, strong, lots of rotation
Pi Between p orbitals Discreet structure, weaker than sigma, no rotation
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Covalent Bonds
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Bonds
In the pi bond of an alkene, the electron pair have:
A. 33% p character and are at a lower energy level than the electron pair in the bond.
B. 33% p character and are at a higher energy level than the electron pair in the bond.
C. 100% p character and are at a lower energy level than the electron pair in the bond.
D. 100% p character and are at a higher energy level than the electron pair in the bond.
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Hybridization
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Hybridization
Remember: All pi bonds are between P orbitals “Leftover” P and S orbitals hybridize,
participate in sigma bonds
Ex: H2C=CH2
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Hybrid Bonds
Suffix C bonds Hybridization
Percent
S:P
Bond Angle
Bond Length
Bond Strength
-ane
-ene
-yne
-yl
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Hybrid Bonds
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 C=C sp 50:50 180 120 835
-yl Side chain
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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
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A) sp2, sp2
B) sp2, sp3
C) sp3, sp3
D) sp3, sp2
For the molecule 1,4 pentadiene, what type of hybridization is present in carbons # 1 and # 3 respectively?
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VSEPR: molecular geometry
valance shell electron pair repulsion GEOMETRY = Minimize electron repulsion
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molecule Lewis structure Shape molecule Lewis structure Shape
BeCl2 Linear, sp
SF4 Seesaw SO3Trigonal
planar, sp2
ICl3 T shaped NO2- Bent
CH4 Tetrahedral, sp3 NH3Trigonal
Pyramidal
PCl5
Trigonal bipyramidal,
dsp3
SF6Octahedral,
d2sp3
IF5 Square Pyramidal ICl4- Square
Planar
VSEPR1. 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
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NOW LET’S MOVE STUFF AROUND!We’ve seen static properties of atoms and molecules…
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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”
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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
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Stereochemistry
Isomers: same molecular formula, different spatial arrangements
Different spatial arrangements different physical and chemical properties!
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Stereochemistry: Isomers
CONNECTIVITY
Structural (constitutional) isomers: Different connectivity.
C4H10 - Isobutane vs n-butane
Same connectivity, different spatial arrangement: Stereoisomers
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Stereochemistry: Isomers
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 25
Stereochemistry: 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
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Stereochemistry: 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)
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Stereochemistry: Isomers
What kind of isomers are the two compounds below?
A. DiastereomersB. EnantiomersC. Constitutional isomersD. Geometric Isomers
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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 symmetry29
Stereochemistry: Rotating Light
Stereochemistry: Chirality R and S:
1. Assign priority by atomic number If attachments are the same, look at the atoms
2. Orient lowest priority (#4) away from the observer3. 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
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WHAT ABOUT BETWEEN MOLECULES?Now we know everything about what happens WITHIN molecules…
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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
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Intermolecular interactions London Dispersion Forces
Between 2 instantaneous dipoles
Dipole-dipole interactions Dipole-dipole or dipole-induced dipole
Hydrogen Bonds Strongest dipole-dipole interaction
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When albuterol is dissolved in water, which of the following hydrogen-bonded structures does NOT contribute to its water solubility?
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HYDROCARBONS
The first and simplest class of molecules we need to get friendly with for Test Day:
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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!
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Hydrocarbons
# of C Root Name # of C Root Name
1 meth 6 hex
2 eth 7 hept
3 prop 8 oct
4 but 9 non
5 pent 10 dec
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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-butyl sec-butyl
iso-butyl tert-butyl
n-propyl
Iso-propyl
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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.
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Alkanes-Important ReactionsPretty 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 halogenation @ most sub’d C aryl>>>alkene> 3o > 2o > 1o >methyl
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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)
http://www.chem.uh.edu/Courses/Thummel/Chem3331/Notes/Chap3/
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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 ringEquatorial (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
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Cyclohexanes
In a sample of cis-1,2-dimethylcyclohexane at room temperature, the methyl groups will:
A. Both be equatorial whenever the molecule is in the chair conformation.
B. Both be axial whenever the molecule is in the chair conformation.
C. Alternate between both equatorial and both axial whenever the molecule is in the chair conformation
D. Both alternate between equatorial and axial but will never exist both axial or both equatorial at the same time
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REACTIONS!!
Things start getting more exciting once we start substituting H for more interesting functional groups… so let’s get ready for some
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Substitutions
Substitution:
one functional group replaces another
Electrophile: wants electrons, has partial + charge
Nucleophile: donates electrons, has partial – charge
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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
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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
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Substitution and Elimination 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
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Which of the following carbocations is the most stable?
A.CH3CH2CH2CH2
B.CH3CH2CH2CHCH3
C. (CH3)3C
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Substitution and Elimination
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
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Substitution and Elimination
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?)
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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
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Benzene: Substituent Effects
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In what order were the substituents added? How can you tell?
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OXYGEN-CONTAINING COMPOUNDSAnother class of molecules we need to be familiar with:
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Oxygen Containing Compounds
Alcohols Aldehydes and Ketones Carboxylic Acids Acid Derivatives
Acid Chlorides Anhydrides Amides Keto Acids and Esters
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Alcohols
One of the most common reactions of alcohols is nucleophilic substitution. Which of the following are TRUE in regards to SN2 reactions:
I. Inversion of configuration occursII. Racemic mixture of products resultsIII. Reaction rate = k [S][nucleophile]
A. I onlyB. II onlyC. I and III onlyD. I, II, and III
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Alcohols Physical Properties:
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
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AlcoholsNaming
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.
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Alcohols-Oxidation & Reduction
Oxidation
Reduction
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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
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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
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Alcohols to Alkylhalidesvia 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
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In the reaction above, if the reagents in the first step were replaced with LiAlH4, what product would result?
a) c)
b) d)
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OH
OH
OH
O
OH
OH
OHHO
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CarbonylsCarbon double bonded to Oxygen
Planar stereochemistry Partial positive charge on Carbon
(susceptibility to nucleophilic attack) Aldehydes & Ketones (nucleophilic addition) Carboxylic Acids (nucleophilic substitution) Amides
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Aldehydes and Ketones
Physical properties: 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 , unsaturated carbonyls: resonance structures
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Aldehydes and KetonesNaming – 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.
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Aldehydes and Ketones-Acetal and Ketal Formationnucleophilic addition at C=O bond
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Aldehydes and Ketones
Keto-enol Tautomerism: Keto tautomer is preferred (alcohols are more
acidic than aldehydes and ketones).
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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?
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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
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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.
Aldehydes and Ketones-Oxidation (Aldehydes Carboxylic acids)
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Aldehydes and Ketones Organometallic reagents:
Nucleophilic addition of a carbanion to an aldehyde or ketone to yield an alcohol
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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
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Which class of compounds would have a higher boiling point, Acyl Chlorides or Carboxylic Acids? Why?
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Carboxylic AcidsNaming
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.
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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.
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Carboxylic Acids-important reactions
Reduction: Form a primary alcohol LiAlH4 is the reducing agent
CH3(CH2)6COOH CH3(CH2)6CH2OHLiAlH4
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Carboxylic Acids-important reactions
Carboxyl group reactions: Decarboxylation: know that it happens (-CO2)
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Carboxylic Acids-important reactions
Fischer Esterification Reaction: Alcohol + Carboxylic Acid Ester + Water
Acid Catalyzed- protonates –OH to H2O (excellent leaving group)
Alcohol performs nucleophilic attack on carbonyl carbon
These bonds arebroken
H+
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Carboxylic Acids-reactions at two positions
Substitution reactions: keto reactions shown, consider enol reactions
To make ->
SOCl2
or PCl3
Heat, -H2OR'OH, heat,
H+-
R2NH
heatHO-
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Carboxylic Acids-reactions at two positions
Halogenation: enol tautomer undergoes halogenation
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Acid DerivativesNaming
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
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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
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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
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Acid DerivativesTransesterification
Transesterification: exchange alkoxyl group with ester of another alcohol
Alcohol + Ester Different Alcohol + Different Ester
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