mcat - organic chemistry overview
DESCRIPTION
Organic chemistryTRANSCRIPT
Molecular Structure Valence
Carbon – 4 bonds Nitrogen – 3 bonds Oxygen – 2 bonds Halogens – 1 bond
Formal Charge = (Group #) – (# non‐bonding electrons) – (1/2 # bonding electrons)
Index of Hydrogen Deficiency
The NUMBER OF PAIRS of HYDROGENS required to become a SATURATED ALKANE
For Resonance Structures ‐ Atoms must not be moved, only ELECTRONS MOVE
Aromatic Molecules – (4n + 2) π electrons
Hydrogen Bonding – occurs when HYDROGEN is bonded to a HIGHLY ELECTRONEGATIVE ATOM
Conformational Isomers
Not TRUE isomers – different spatial orientations of the same molecule
Chirality‐ A chiral carbon is bonded to FOUR DIFFERENT SUBSTITUENTS
Absolute Configuration
Rectus (to the right) & Sinister (to the left) according to priority
The LARGEST MOLECULAR WEIGHT is the HIGHEST PRIORITY (1)
Hydrogen is always the lowest priority (4) and should be oriented out the back of the page
Relative Configuration
Two molecules have the SAME relative configuration about a carbon if they differ by only ONE
SUBSTITUENT and the other substituents are oriented identically about the carbon
Optical Activity & Observed Rotation
Optically inactive compounds may have
• No chiral centers & Equal amount of both stereoisomers (a racemic mixture)
Optically Active compounds can be
1) + / d – rotates light CLOCKWISE
2) ‐ / l – rotates light COUNTER‐CLOCKWISE
Structural Isomers
1) Same molecular formula
2) DIFFERENT BOND‐TO‐BOND CONNECTIVITY
3) Isobutane (C4H10) vs. n‐butane (C
4H10)
4) Are NOT THE SAME MOLECULE
Stereoisomer SUBTYPE ‐ Enantiomers
1) Same molecular formula
2) Same bond‐to‐bond connectivity
3) MIRROR IMAGES OF EACH OTHER
4) Are NOT THE SAME MOLECULE – opposite absolute configurations at chiral centers
Same chemical and physical characteristics except for
1) Reactions with other chiral compounds
2) Reactions with polarized light
Stereoisomer SUBTYPE ‐ Diastereomers
1) Same molecular formula
2) Same bond‐to‐bond connectivity
3) Are NOT MIRROR IMAGES OF EACH OTHER
4) Are NOT THE SAME MOLECULE
Geometric Isomers (a special type of diastereomer)
• Cis‐isomers & Trans‐isomers
Meso Compounds
1) When TWO chiral centers OFFSET EACH OTHER
2) Optically Inactive
3) PLANE of SYMMETRY divides compound into two halves that are mirror images
Stronger Dipole Moment
Stronger Intermolecular Forces
Higher Boiling Points
Higher Energy Level – Higher Heat of Combustion
Functional Groups
Alkane H3C – CH
3 Alcohol R – OH
Alkene H2C = CH
2 Ether R – O – R
Alkyne HC ≡ CH Amine R – NH2 R
2 – NH R
3 – N
Aldehyde Ketone Carboxylic Acid Ester Amide
Alkyl R Halogen [‐X] ‐F / ‐Cl / ‐Br / ‐I
Hydroxyl ‐ OH Geminal‐dihalide
Alkoxy ‐ OR Vicinal‐dihalide
Hemiketal R | R | OR | OH
Ketal R | R | OR | OR
Hemiacetal H | R | OR | OH
Acetal H | R | OR | OR
Mesyl Group (Ms‐) Tosyl Group (Ts‐)
H | R | OR | OH
Carbonyl Acyl Anhydride
Aryl Benzyl Hydrazine Hydrazone
Vinyl Allyl Nitrile Epoxide
Enamine Imine Oxime Nitro Nitroso
Hybridization Bond Angles Shape sp 180° Linearsp2 120° Trigonal Planarsp3 109.5° Tetrahedral, Pyramidal, or Bent
Hydrocarbons, Alcohols, & Substitutions
Alkanes
Methyl ‐CH3 Primary ‐CRH
2 Secondary ‐CR
2H Tertiary ‐CR
3
Lowest Density of all groups of organic compounds
Methane, Ethane, Propane, and Butane are gases at room temperature
INCREASED Molecular Weight | INCREASED Boiling Point | INCREASED Melting Point
INCREASED Branching | DECREASED Boiling Point | INCREASED Melting Point
Cyclo‐Alkanes
CHAIR and BOAT conformations
Large Substituents are MORE STABLE in the EQUATORIAL POSITION
Combustion (radical & exothermic reaction)
CH4 + 2 O
2 + energy CO
2 + 2 H
2O + heat
COMBUSTION is a RADICAL REACTION
HEAT OF COMBUSTION – change in enthalpy of a combustion reaction
Halogenation (radical & exothermic reaction)
Alkanes will react with HALOGENS in the presence of heat or light to form a FREE RADICAL
HOMOLYTIC CLEAVAGE – bond is broken with one electron going with each atom
1) INITIATION
a. Halogen is diatomic molecule, and HOMOLYTIC CLEAVAGE results in 2 free radicals
2) PROPAGATION
a. HALOGEN RADICAL removes hydrogen from alkane, creating an ALKYL RADICAL
b. ALKYL RADICAL reacts with diatomic molecule creating ALKYL HALIDE and a NEW HALOGEN
RADICAL
3) TERMINATION
a. TWO RADICALS BOND or RADICAL bonds to the wall of the container to end the chain reaction
Stability of ALKYL RADICALS: 3° > 2° > 1° > methyl
Fluorine – VERY REACTIVE, major product is PRIMARY
Chlorine – REACTIVE, major product is whatever is LEAST STERICALLY HINDERED
Bromine – SELECTIVE, major product is TERTIARY
Dehydration of an alcohol (E1 Reaction)
Alcohol + hot concentrated H2SO
4 Alkene + H
2O + HSO
4
‐
Saytzeff Rule – MAJOR product of ELIMINATION is the MOST SUBSTITUTED ALKENE
Dehydrohalogenation (E1 or E2 Reaction)
E1 Mechanism – WITHOUT a strong base – 2 steps – unimolecular (substrate only)
1) Halogen drops off forming a CARBOCATION
2) Hydrogen is removed leaving alkene
E2 Mechanism – STRONG BULKY BASE – 1 step – bimolecular (substrate & nucleophile)
1) Base REMOVES a hydrogen adjacent to the halogen
2) Halogen drops off leaving alkene
In ELIMINATION, base pulls off a hydrogen
In SUBSTITUTION, nucleophile attacks carbon
Catalytic Hydrogenation (addition reaction)
• Heterogeneous catalyst (Ni / Pd / Pt) promotes SYN addition
• Hydrogenation is EXOTHERMIC with high energy of activation
Oxidation Of Alkenes
OZONOLYSIS – ozone is VERY reactive, breaking right through alkenes and alkynes
Alkenes INTO two CARBONYL GROUPS
Alkynes INTO two CARBOXYLIC ACIDS
Electrophilic Addition
Electrophiles – attracted to electrons –POSITIVELY CHARGED & Alkenes are ELECTRON‐RICH
When HF / HCl / HBr / HI are added to an alkene:
Markovnikov’s rule – the hydrogen will add to the carbon with the MOST HYDROGENS
HBr & Peroxides (ROOR) add to alkenes ANTI‐MARKOVNIKOV
Hydration of an Alkene
Alkene + cold dilute H2SO
4 + H
2O Alcohol
Oxymercuration / Demercuration
1) Oxymercurial ion attacks alkene, forming triangular mercury complex
2) H2O attacks ANTI‐ to form an ALCOHOL, losing the mercury group
3) If ROH is used instead of water, an ETHER is formed
Hydroboration
Alkene + BH3 + peroxide Alcohol (anti‐markovnikov)
Halogenation Of An Alkene
Br2 and Cl
2 add ANTI‐ to alkenes to form VIC‐DIHALIDES
Benzene
• Undergoes SUBSTITUTION, not addition
• Flat molecule, stabilized by RESONANCE
• Ortho / Meta / Para
Electron Donating Groups (ACTIVATES the Ring)
STRONGLY donating (ortho‐ / para‐ directing)
‐O‐ ‐OH ‐NR2
MODERATELY donating (ortho‐ / para‐ directing)
‐OR
WEAKLY donating (ortho‐ / para‐ directing)
‐R
Electron Withdrawing Groups (DEACTIVATES the Ring)
STRONGLY withdrawing (meta‐ directing)
‐NO2 ‐NR
3+ ‐CCl
3
MODERATELY withdrawing (meta‐ directing)
‐Carbonyls ‐SO3H ‐CN
WEAKLY withdrawing (ortho‐ / para‐ directing)
Halogens
SN1 (substitution / nucleophilic / unimolecular)
1) Hydrogen drops off forming a CARBOCATION – rate determining step
2) Nucleophile attacks the carbocation
SN2 (substitution / nucleophilic / bimolecular)
1) Nucleophile attacks substrate from behind – knocks leaving group free while binding to substrate
Nucleophilicity
A BASE is a stronger NUCLEOPHILE than its conjugate acid, but a BASE is NOT NECESSARILY a NUCLEOPHILE
If a NUCLEOPHILE behaves as a BASE, ELIMINATION RESULTS
LESS BULKY NUCLEOPHILE, with NEGATIVE CHARGE & POLARIZABILITY add to
nucleophilicity
Solvents
POLAR PROTIC SOLVENTS – stabilize the nucleophile and any carbocation that forms
INCREASE SN1 SPEED DECREASE S
N2 SPEED
POLAR APROTIC SOLVENTS – cannot form hydrogen bonds
INCREASE SN2 SPEED DECREASE S
N1 SPEED
Leaving Groups
The best leaving groups are those that are STABLE WHEN THEY LEAVE
The WEAKER the BASE, the BETTER the LEAVING GROUP
SN1 vs. SN2
SN1 SN2 Nucleophile N / A Strong NucleophileSubstrate 2° / 3° Methyl / 1° / 2° (unhindered)Solvent Polar solvent increases rate Polar solvent DECREASES rateSpeed [Substrate] [substrate] [nucleophile]
Stereochemistry Creates RACEMIC mixture INVERTS around chiral centerSkeleton Maybe skeletal rearrangement NO rearrangement
Alcohols
BP goes up with increasing Molecular Weight
ROH hydrogen bonds, dramatically raising MP and BP
Alcohols can behave as ACIDS, with methyl –OH being the STRONGEST ACID
Grignard Synthesis of Alcohols
Oxidation Of Alcohols
Oxygen‐Hydrogen ratio INCREASES – Oxidation occurred
Oxygen‐Hydrogen ratio DECREASES – reduction occurred
The Pinacol Rearrangement
In VICINAL DIOLS, DEHYDRATION product is a KETONE or ALDEHYDE
Ethers
ALMOST ALWAYS THE ANSWER to SOLVENT QUESTIONS on the MCAT
ROR + HBr ROH + RBr
Acidities Of Functional Groups
Alkane Alkene Hydrogen Ammonia Alkyne ALDEHYDE Alcohol Water CARBOXYLIC ACID
Carbonyls & Amines
The Carbonyl
Carbon DOUBLE BONDED to oxygen PLANAR Stereochemistry PARTIAL POSITIVE on the carbon
Aldehydes & Ketones
ALDEHYDE R – (C=O) – H KETONE R – (C=O) – R
FORMALDEHYDE H – (C=O) – H ACETONE CH3 – (C=O) – CH3
Lower Boiling Point than ALCOHOL
α‐carbon is VERY ACIDIC – loses a proton to become an ENOLATE ION (stabilized by resonance)
In β‐dicarbonyls, the ENOLATE IONIC form is more prevalent
KETO‐ENOL Tautomerization
Formation of Acetals
KETONE + ALCOHOL HEMIKETAL + ALCOHOL KETAL
ALDEHYDE + ALCOHOL HEMIACETAL + ALCOHOL ACETAL
Acetals / Ketals can act as BLOCKING GROUPS
to PRESERVE a CARBONYL GROUP
Aldol Condensation
Aldehyde + Aldehyde Ketone + Ketone Aldehyde + Ketone
α‐hydrogen is abstracted, forming an ENOLATE ION
α‐carbon of ENOLATE attacks carbonyl carbon of other molecule, forming ALKOXIDE ION
ALKOXIDE ION grabs a hydrogen to become an ALDOL (aldehyde & alcohol)
Halogenation & Haloform Reaction
HALOGENS add to KETONES at the α‐carbon in presence of acid or base
METHYL KETONE with BASE, the α‐carbon is COMPLETELY HALOGENATED
HALOFORM breaks off (CHCl3 / CHBr3 / CHF3) leaving CARBOXYLATE ION
Wittig Reaction
Ketone / Aldehyde + Ylide (carbanion) ALKENE
α‐β Unsaturated Carbonyls
Also called 1,4‐addition – adding HX forms ENOL TAUTOMER and then KETO
Carboxylic Acids
Carboxylic Acid R‐COOH Formic Acid H – COOH
Benzoic Acid C6H5 ‐ COOH Acetic Acid CH3 – COOH
If the name ends in –ate R – COO‐
Make STRONG HYDROGEN BONDS – to form dimmers
This effectively doubles M.W. – significantly increasing B.P.
Decarboxylation
CARBOXYLATE ION LOSES CO2 to become KETO‐ENOL TAUTOMERS
Carboxylic Acid Derivatives – ACYL CHLORIDES
MOST REACTIVE OF ALL CARBOXYLIC ACID DERIVATIVES
ACID CHLORIDE + H2O CARBOXYLIC ACID + HCl
ACID CHLORIDE + ROH ESTER + HCl
ACID CHLORIDE + RNH2 AMIDE + HCl
ACID CHLORIDE + RCOOH ANHYDRIDE + HCl
ACID CHLORIDE + H2O CARBOXYLIC ACID + HCl
ESTER + H2O CARBOXYLIC ACID + ROH
AMIDE + H2O CARBOXYLIC ACID + RNH2
ANHYDRIDE+ H2O CARBOXYLIC ACID + RCOOH
ALDEHYDES / KETONES Nucleophilic ADDITION
CARBOXYLIC ACIDS / DERIVATIVES Nucleophilic SUBSTITUTION
Carboxylic Acid Derivatives ‐ ESTERIFICATION
Carboxylic Acid Derivatives ‐ TRANSESTERIFICATION
Carboxylic Acid Derivatives – ACETOACETIC ESTER SYNTHESIS
ACETOACETIC ESTER + RX + H+ / HEAT KETONE + CO2
Carboxylic Acid Derivatives ‐ REACTIVITIES
Amide Ester Carboxylic Acid Acid Anhydride Acyl Chloride
Amines
Ammonia ‐NH3
Amine Degree depends on number of ATTACHED –R GROUPS
1) Act as LEWIS BASE – DONATING LONE PAIR OF ELECTRONS
2) Act as a NUCLEOPHILE where LONE PAIR of ELECTRONS attacks POSITIVE CHARGE
3) Nitrogen can take on a FOURTH BOND (+)
4) Nitrogen can HYDROGEN‐BOND – increasing BOILING POINT and SOLUBILITY
Condensation with Ketones
AMINE + ALDEHYDE / KETONE WATER + IMINE / ENAMINE
Wolff‐Kishner Reduction
HYDRAZINE + ALDEHYDE / KETONE ALKANE + WATER + N2
Alkylation of Amine
Hofmann Elimination
Amines & Nitrous Acid
NITROUS ACID + 1° AROMATIC AMINE DIAZONIUM ION
The Diazonium Group is EASILY REPLACED
Amides
Acetamide N‐ethylacetamide
β‐Lactams (CYCLIC AMIDES)
Hofmann Degradation
Phosphoric Acid
When heated, phosphoric acid forms PHOSPHORIC ANHYDRIDES
Tri‐phosphates exist as negative ions, such as ATP
Biochemistry & Lab Techniques
Fatty Acids
LONG CARBON CHAIN WITH COOH on the end
Amino Acids
Zwitterion – DIPOLAR ION (one side – and one side +)
BASIC AMINO ACIDS
Histidine
Arginine
Lysine
ISOELECTRIC POINT – the pH where 100% of the amino acids are ZWITTERIONS
Carbohydrates
1) GENERAL FORMULA Cn(H
2O)
n
2) Can have either ALDEHYDE or KETONE groups to be called ALDOSE or KETOSE
3) ANOMERIC CARBON – the ONLY CARBON attached to TWO OXYGENS
Lab Techniques
SPECTROSCOPY
• Nuclear Magnetic Resonance (NMR)
• Infrared Spectroscopy (IR)
• Ultraviolet Spectroscopy (UV)
SPECTROMETRY
• Mass Spectrometry
SEPARATION TECHNIQUES
• Chromatography
• Distillation
• Crystallization
• Extraction
NMR
1) Each peak is a CHEMICALLY‐EQUIVALENT HYDROGEN
2) SPLITTING PEAKS is created by NEIGHBORING HYDROGENS as by n+1 (n = # of neighboring carbons)
3) To the LEFT is DOWNFIELD (unshielded by electronegative atoms)
IR Spectroscopy
CARBONYL GROUP 1700
‐OH GROUP 3200 – 3600
Ultraviolet Spectroscopy
UV starts around 220 nm (butadiene)
1) Each additional CONJUGATED BOND adds 30‐40 nm to the wavelength ABSORBED MOST
Visible Spectrum
• If compound has 8+ CONJUGATED DOUBLE BONDS, its absorbance enters the VISIBLE SPECTRUM
• β‐Carotene has 11 CONJUGATED DOUBLE BONDS, with an absorbance of about 500 nm
• β‐Carotene absorbs the BLUE‐GREEN color of 500 nm, and displays the COMPLEMENTARY COLOR of red‐
orange
Mass Spectrometry
• Mass Spectrometry gives the MOLECULAR WEIGHT
• Sample molecules are bombarded by electrons, causing them to break apart and IONIZE
• Ions are accelerated through a magnetic field, most are +1
• RADIUS OF CURVATURE depends upon the MASS to CHARGE RATIO (m/z)
• BASE PEAK – the largest peak
• PARENT PEAK – the peak made by the molecular ion (same as ORIGINAL MOLECULE but without ONE
ELECTRON so it has a +1 charge)
Chromatography
• Separation of a mixture by passing it over or through a matrix that ADSORBS different compounds with
DIFFERENT AFFINITIES
• MOBILE PHASE / STATIONARY PHASE
• The MORE POLAR compound moves more SLOWLY because it binds to the POLAR STATIONARY PHASE
Distillation
• Separation based upon VAPOR PRESSURE
• Separates a solution of two volatile liquids with a BOILING DIFFERENCE of at least 20° C
• The compound with the LOWER BOILING POINT (HIGHER VAPOR PRESSURE) will boil off and can be
captured
Crystallization
• Works on the principle that PURE SUBSTANCES FORM CRYSTALS more easily than impure substances
• Crystallization is VERY INEFFICIENT
Extraction
• Based on SOLUBILITY DUE TO SIMILAR POLARITIES
• LIKE DISSOLVES LIKE