MCAT Organic Chemistry

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  1. Hybrid Orbitals: types, compositions, and geometries as they relate to σ and π bonds
    • 1 s and 3 p orbitals combine to make 4 sp3 orbitals and 4 σ bonds in an approximately tetrahedral shape, 109.5o separation (ex. CH4)
    • 1s + 2p orbitals make 3 sp2 orbitals which will make 3 σ bonds with 120o separation in a trigonal planar shape leaving one p orbital to participate in a π bond (ex. H2C=CH2)
    • 1s + 1p orbital makes 2 sp orbitals which make 2 σ bonds at 180o separation in a linear shape leaving 2 p orbitals to participate in π bonds (ex. alkynes like HCΞCH)
  2. VSEPR (valence shell electron-pair repulsion) theory
    • Used to predict the shapes of molecules
    • based on the idea that electron pairs will spread out as much as possible
    • Double and triple bonds act as a single contribution (so O=C=O only has 2 which will make 180o separation and be linear)
    • Lone pairs and pairs in bonds count but lone pairs are actually stronger because they are closer to the nucleus of the atom of interest
    • H2O is not linear because of the 2 lone pairs on oxygen --> bent (orbitals are approximately tetrahedral)
    • NH3 is not trigonal planar because of the lone pair on N --> pyramidal (orbitals of N are also approximately tetrahedral)
    • BF3 is trigonal planar because B does not have any lone pairs, just 3 pairs in bonds with 120o separation
  3. Delocalized electrons and resonance
    • Delocalized electrons are electrons that do not explicitly belong to any one atom or bond in a molecule
    • Often π bond electrons fall into this category, especially in ionic structures
    • Best example, a C6 (benzene) ring contains 6 delocalized electrons drawn as a circle inside the ring meaning that 2 resonance structures are equally possible for the positions of the π bonds.
  4. Multiple bonding effects on bond length, bond energies, and structure rigidity
    • a pi bond is weaker than a sigma bond (thus a double bond is not twice as strong as a single bond)
    • more bonds makes the total bond shorter and stronger (even though each component is weaker)
    • rigidity is increased because only single bonds rotate freely (even partial double bonds like the peptide bond prevent free rotation)
    • rare quadruple bonds contain 1 sigma, 2 pi, and 1 delta bond, only form between transition metals
  5. Types of Isomers and basic definition
    • Isomers have the same molecular formula but different structural formulas
    • Constitutional isomers (structural isomers) have different connectivity: Positional have same fxn'l groups positioned differently & Functional have different fxn'l groups
    • Geometric isomers (cis/trans; Z/E; R(D)/S(L)): have same connectivity but differ in arrangement
    • Stereoisomers (enantiomers & diastereomers): have chiral carbon(s) with R(D)/S(L) designations
    • Enantiomers: every chiral carbon is opposite
    • Diastereomers: not all, but some chiral carbons are different
  6. Conformational Isomers compare the state of eclipse of 2 connected chiral carbons; 4 types + 3 ring configurations; general rules
    • In decreasing amounts of torsional strain (increasing stability):
    • syn-periplanar - bulky groups eclipse each other
    • anticlinal eclipsed - bulky groups eclipse H
    • Gauche - bulky groups staggered @ 60o
    • Anti - bulky groups staggered @ 180o
    • 3 ring conformations in increasing stability:
    • Boat - everything is eclipsed
    • Twist boat - not completely eclipsed or completely staggered
    • Chair - everything staggered
    • *Technically not isomers because change due to rotation of bonds (not breaking), call them conformers
  7. Light polarization and specific rotation
    • polarized light = all EM fields in one direction
    • optically active chiral centers rotate polarized light left or right (relative)
    • Left rotation: (-) = l = levorotatory
    • Right rotation: (+) = d = dextrorotatory
  8. Steps to determine R(D)/S(L) configuration of a chiral carbon
    • 1) Identify chiral carbon
    • 2) assign group priorities based on the molecular weight of the atoms directly bonded to carbon, then extending outward as necessary
    • 3) rotate lowest priority to the back
    • 4) draw an arrow pointing from highest to lowest priority, arrow turns right = (R), arrow turns left = (S)
  9. Racemic mixtures (definition) and separation
    • Definition: mixture contains equal amounts of both enantiomers (also called racemate)
    • Separation (chemical): convert to diastereomers, separate based on (now) different physical properties, & convert back to enantiomers
    • Separation (biological): Enzymes are highly D/L specific
  10. IR Spectroscopy: Basic features and common group absorption fingerprints
    • Plotted as transmittance vs wavenumber (cm-1, correlates with frequency), dips represent absorbance
    • ~3000 cm-1 usually involves an H atom (O-H, N-H, C-H)
    • <~2000 cm-1 does not involve H (same atoms with higher bond order -> higher wavenumber)
    • 1700 cm-1 = carbonyl
    • 3300 cm-1 is either O-H, N-H, or ΞC-H (broader peaks due to H-bonding means these increase in sharpness left to right)
    • <1300 cm-1 = fingerprint region unique for each compound
  11. Visible Region: Primary colors of light and pigment and the universal indicator
    • Light: Red + Green + Blue -> White (none=black)
    • Pigment (complimentary to light): Yellow + Cyan + Magenta -> Black (none = white)
    • absorption of light -> complimentary color
    • Universal Indicator (for pH): Red (very acidic) -> green (neutral) -> purple (very basic)
  12. UV absorption uses
    • pi bonding and non-bonding electrons absorb UV light and transition to anti-bonding orbitals
    • Conjugated double bonds decrease energy of EM radiation absorbed -> longer wavelengths (closer to visible spectrum)
  13. Mass Spectrometry: Basic principles and Uses
    • Fragment molecule to ions with high energy electrons and separate fragments based on mass/charge (m/e or m/z) ratio by a magnetic field
    • Parent peak: highest m/z ratio, not fragmented
    • Base peak: most abundant species
    • Isotopes: small peaks near real peaks
    • Uses: MW of a molecule, Identify molecule by fragmentation patterns, or Identify heteroatoms by their characteristic isotope ratios
  14. 1H-NMR (Nuclear Magnetic Resonance) Spectroscopy: Basic principles
    • Protons spin, in a magnetic field, spin lines up with lowest energy; radiowaves of a specific frequency can excite specific (equivalent) protons to "flip" by absorption called resonance
    • Chemical Shift: (Resonance frequency of absorption) depends on degree of electron shielding (affected by electronegativities of nearby atoms, especially bonded atoms), More shielding (less electronegative neighbor) creates only a small shift and peak appears upfield (to the right) and vice versa
    • Higher numbers of equivalent protons produce 1 signal at height n x signal for one proton
    • measured relative to TMS (tetramethylsilane) standard in ppm
    • Spin-spin splitting occurs when the magnetic fields of neighboring (3 bonds away) protons influence chemical shift -> split into n+1 peaks (n=# of neighboring H+); protons across double bonds split farther
  15. Separations and Purifications: Extraction, Distillation, Chromatography, and Recrystallization
    • Extraction: 2 immiscible liquids (e.g. Organic and Aqueous phases)
    • Distillation: Separate liquids based on boiling point
    • Chromatography: Mobile phase moves along stationary phase dragging solutes along with different affinities (Gas-liquid, Paper, & thin-layer)
    • Recrystallization: make a warm saturated solution and allow to cool -> recrystallize; choose a solvent where solute is soluble at high temps but not cooler temps but impurities are highly soluble at cool temps
  16. Free radical chain reaction mechanism
    • dependent on the presence of free radicals
    • inhibited by antioxidants
    • alkane + halogen + free radical initiator (UV light or Peroxides) -> alkyl halide
    • more subtituted radicals are more stable (3o >2o >1o> methyl) -> substitution will occur at the more substituted carbon
  17. Alcohols: Properties and General Principles
    • Nomenclature: hydroxyl or hydroxy prefix or -ol suffix
    • H-bonding -> higher boiling point, water soluble, Broad IR peak at 3300cm-1
    • R-OH pKa = 15, Ar-OH pKa=10
    • More chain branching -> higher Tm but lower boiling point
  18. Substitution Reactions involving Alcohols
    • R-OH + HX ↔ R-X + H2O
    • SN1: involves a carbocation intermediate (OH leaves as H2O before X- comes in); occurs if stable carbocation can be formed, usually a tertiary carbon center and a protic solvent
    • SN2: involves a transition state where -OH and -X are both partially bonded to central carbon; preferable if carbocation is unstable; usually at a primary carbon center and/or in aprotic but polar solvent
    • Both require a good leaving group
  19. Oxidation Reactions involving Alcohols (central vs terminal, weak vs strong oxidizers)
    • Central -OH: not bonded to a terminal carbon, will be oxidized to a ketone group
    • Terminal -OH: bonded to a terminal carbon, will be oxidized first to an aldehyde (weak oxidizers stop here) then to a carboxylic acid by strong oxidizers like KMnO4 or CrO3
  20. Pinacol Rearrangement in polyhydroxyalcohols
    H2SO4 (acid) and heat cause protonation of R-OH to R-OH2+ which leaves creating a carbocation that will rearrange the methyl (opposite the other -OH) and the other -OH converts to =O (ketone, possibly aldehyde?)
  21. Protection of Alcohols
    • trimethylsilyl group (Cl-SiMe3) + R-OH → R-O-SiMe3
    • Can be unprotected by removal with fluoride, R-O-SiMe3 + F- → R-OH + F-SiMe3
  22. SOCl2 and PBR3 reactions with Alcohols
    • R-OH + SOCl2 → R-Cl (SO2 + HCl)
    • R-OH + PBr3 → R-Br (H3PO3 + R3PO3 + HBr)
    • Replace -OH with halogen
  23. Mesylate and Tosylate ions (Sulfonates) react with Alcohols
    • H3C-SO2-Cl + HO-R → H3C-SO2-O-R (Mesylate)
    • Alcohol + Tosyl chloride (TsCl) → Tosylates
    • Sulfonates (R-SO3-) are good leaving groups
  24. Esterification of Alcohols
    • Acid + Alcohol → Ester
    • R-COOH + HO-R' → R-COO-R'
  25. Inorganic Esters from Alcohols
    • Phosphates and Sulfonates are inorganic esters
    • PBr3 + 3R-OH → H3PO3 + 3 RBr
    • Intermediates are P(OR)3 and H-Br and ionized Br- replaces each R group sequentially
    • SOCl2 + ROH → SO2 + HCl + RCl through a similar mechanism
    • Basically using the ROH as a source of oxygen and switching halogens for oxygen
  26. Nucleophillic attack on an aldehyde or ketone
    • Alcohol + Adehyde -> hemiacetal (1 equivalent) -> acetal (2 equivalents of alcohol); same for hemiketal/ketal
    • Hemiacetal/ketal = C with an -OH and an Ether
    • Acetal/Ketal = C with 2 ethers
  27. Imine/Enamine synthesis from and aldehyde or ketone
    • Primary amine (R-NH2) + aldehyde or ketone ->imine
    • 2o amine (R-NH-R') + aldehyde or ketone -> enamine (R"-C-C=O becomes R"-C=C-N-R&R')
    • Replacing carbonyl with either double bond to N (imine) or single bond to N and double bond to neighboring C (enamine)
  28. Haloform reactions adjacent to a ketone carbonyl
    • ketones + halogen -> halogenation of α-Carbon
    • methyl-ketone + halogen -> haloform (CHX3) + Carboxylate
    • Halogenation can be partial or complete (all H replaced with X, works because neighboring O can temporarily accept the charge if alpha carbon is deprotonated)
    • Second reaction occurs due to nucleophillic attack on carbonyl carbon after complete halogenation of methyl-alpha-C; b/c trihalogenated is a good leaving group
  29. Aldol Condensation of Methyl-Ketone
    • Key feature is the acidic alpha-H+
    • Example: 2 acetaldehyde (HC=OCH3) will condense to HC=O-C=CH-CH3)
    • Deprotonation of acetaldehyde creates nucleophile that attacks carbonyl-C of another acetaldehyde displacing one of the carbonyl bonds to O (creating -OH-) which will leave as water and C will double bond with central C (closer to remaining carbonyl)
  30. 1,3-dicarbonyl compounds, also called active methylene compounds
    • R-C=O-CH2-C=O-R' -> R-COH=CH-C=O-R'
    • This experiences the tautomeric form: R-C=O-CH=COH-R' where each carbonyl is switching between keto- and enol- forms
    • Structure is stabilized by intramolecular H-bonding
  31. Keto-enol Tautomerism
    • Keto is the more stable, predominant form
    • R-CH-C=O-R' (keto) ↔ R-C=COH-R' (Enol)
  32. Organometallic Reagents react with aldehydes/ketones
    • Organometallic compounds create R- in solution which attacks C=O -> R-C-OH
    • Create C-C bonds
    • R-X + Li -> R-Li (and Li-X)
    • R-X + BuLi -> R-Li (and BuX)
    • R-Li + C=O -> R-C-OH (wherever the carbonyl was in the original molecule)
  33. Wolff-Kishner reaction
    • Reduces C=O to -CH2-
    • C=O + H2N-NH2 -> -CH2- + N2
  34. Gringard Reagents
    • Just like organometallics -> R-
    • R-X + Mg -> R-Mg-X
    • R-Mg-X + C=O -> R-C-OH
  35. Aldehydes and Ketones: Nomenclature, Physical Properties, and General Principles
    • Nomenclature: aldehyde suffix -al or -aldehyde; ketones prefix keto- or oxo- suffix -one
    • Physical Properties: C=O is polar, boiling points between alkanes and alcohols/carboxylic acids; IR spectrum 1700 cm-1
    • General Principles: substituents contribute to steric hindrance (bulky groups around C=O block access to electrophillic C and decrease reactivity); alpha-H+ acidity means carbanions are stabilized by resonance; alpha-beta unsaturated carbonyls have resonance structures (nucleophile such as -OH easily added at beta position)
  36. Carboxylic Acids: Nomenclature, Physical Properties, and General Principles
    • Nomenclature: suffix -oic acid, -dioic acid
    • Physical Properties: increased boiling point (H-bonding), soluble in water, IR peaks at 1700 (for C=O) and 3300 (for -OH)
    • General Principles: H-bonding contributes to dimerization, pKa ≃ 5 (weak acid), substituents with an electron withdrawing group are inductive (make acid stronger); Conjugate base is resonance stabilized
  37. Nucleophillic Attack on -COOH
    • Nucleophile + R-COOH -> R-C=O-Nuc
    • Example: peptide bond
  38. Nucleophillic attack by -COOH
    • R-COOH + SOCl2 -> R-C=O-Cl (SO2 + HCl)
    • carboxylic hydroxyl oxygen is a nucleophile and can attack electrophiles like the S in SOCl2 but the resulting chloride ion will attack the electrophillic C and displace the -O-S=O-Cl as SO2 and Cl-
  39. Reduction of -COOH
    Can be reduced to an alcohol by LiAlH4
  40. Decarboxylation of Beta-keto acids
    • Spontaneous in a neutral or basic environment
    • R-C=O-CH2-COO- -> R-CO-=CH2 + CO2 -> R-C=O-CH3 (deprotonates water)
  41. Halogenation at alpha (2) position of a carboxylic acid
    • convert to enolizable form: R-CH2-COOH + PBr3 -> R-CH2-C=OBr
    • Enolize: R-CH=COHBr
    • Halogenation: R-CH=COHBr + Br2 -> R-CHBr-C=O-Br
    • Revert (hydrolysis): R-CHBr-COOH
  42. Substitution at alpha (2) position of a carboxylic acid
    RCOOH + E+ -> substitution at alpha carbon
  43. Acid Derivatives: 4 types, Nomenclature, Example of each, Physical Properties and General Principles
    • Acid Chlorides: -oyl chloride (ex. ethanoyl chloride H3C-C=O-Cl); IR C=O @ ~1800
    • Anhydrides: -oic anhydride (ex. ethanoic anhydride H3C-C=O-O-C=O-CH3); IR 2 C=O as 2 bands between 1700-1800
    • Amides: -amide (ex. N-methyl ethanamide H3C-C=O-NH-Me); IR N-H @ ~3300 and C=O ~1700
    • Esters: -oate (ex. methyl ethanoate H3C-C=O-O-Me); IR C=O @ 1700 and Ether (C-O) ~1200
    • Physical Properties: C=O dipole interactions (no H-bonding w/o polar H) but still increase boiling point, Amides also H-bond b/c N-H group (like peptide backbone)
    • Relative Reactivity: Acid Chloride (halides are a good leaving group) >Anhydride >Esters >Amides (peptide bonds, most stable b/c NR2- is a terrible leaving group and C-N partial double bond character)
    • Steric Effects: bulky groups around C=O help protect from nucleophillic attack
    • Electronic Effects: groups (like COO-) that redistribute and stabilize negative charges are good leaving groups, why anhydrides >esters
    • Strain: C-N bond cannot rotate (high strain in a ring); ex. beta-lactam is a 4 member ring with 1 amide and high strain
  44. Preparation of Acid Chloride
    • R-COOH + SOCl2 -> R-C=O-Cl
    • *see nucleophillic attack by -COOH
  45. Preparation of Anhydride (2 ways)
    • Heat: R-COOH + R'-COOH -> Anhydride + H2O
    • Acid chloride + R-COOH + base -> anhydride: R'-C=O-Cl + R-COOH -> R'-C=O-O-C=O-R + HCl
  46. Preparation of an Ester
    • Acid chloride + alcohol + base -> ester
    • R-C=O-Cl + R'-OH + base -> R-C=O-O-R'
    • *Similar to esterification but with acid chloride instead of -COOH
  47. Preparation of an Amide
    • Acid chloride + Amine -> Amide
    • R-C=O-Cl + H2N-R' -> R-C=O-NH-R'
  48. Destruction of Acid Chloride
    Acid chloride + water -> -COOH + HCl
  49. Nucleophillic Substitution on an Acid Derivative
    • R-C=O-X + Nucleophile -> R-C=O-Nuc
    • X=Cl >anhydride >ester >amide (b/c X needs to be a good leaving group)
  50. Hofmann Rearrangement of an Amide
    • Amide loses C=O: R-C=O-NH2 + Br2 + Base -> R-NH2
    • Base deprotonates NH2
    • Br binds negative N
    • Base deprotonates NHBr
    • Br leaves negative N (takes e- with it)
    • Alkyl migration (nucleophillic N with 2 lone pairs of e- attacks carbonyl C, displacing R-C bond to N) creates Isocyanate O=C=N-R
    • Isocyanate + base will pick up OH- then decarboxylate to NH2-R
  51. Transesterification
    • Ester + Alcohol -> new Ester
    • R-C=O-O-R' + HO-R" -> R-C=O-O-R" + R'-OH
    • Alcohol attacks carbonyl C (similar to Acid + Alcohol -> Ester reactions)
  52. Hydrolysis of fats and Glycerides (Saponification)
    • R-C=O-O-R' + NaOH -> R-C=O-O- Na+  + R'OH
    • Splits Triglyceride into glycerol (R'(OH3) + fatty acids
  53. Hydrolysis of Amides
    • Leaving group must be the neutral amine, NOT NH2-
    • R-C=O-NH-R' attacked by OH- becomes R-CO(-)OH-NH-R'
    • C-N electrons leave C for H in water creating R-COOH + H2N-R' and regenerating OH-
  54. Keto acids and esters: Nomenclature & General Principles
    • Alpha-keto acid: (R-C=O-COOH) is 2-oxo acid (ex. alpha-ketopropanoic acid = 2-oxopropanoic acid)
    • Beta-keto acid: (R-C=O-CH2-COOH) is 3-oxo acid
    • Beta (Alpha)-keto esters: R-C=O-CH2-COO-R' is 3 (2) -oxo ester (ex. methyl-beta-ketobutanoate = methyl 3-oxobutanoate)
    • General Principles: hydrogen adjacent to carbonyl group is more acidic and the alpha H of the beta-keto ester is even more acidic between 2 C=O
  55. Decarboxylation of a beta-keto ester
    • beta-keto esters -> beta-keto acids -> enols -> ketos
    • Easy because enol stabilizes rxn intermediate (not so for alpha but didn't go in to it in the review)
    • Ester Hydrolysis: R-C=O-CH2-COO-R' (Acid + Heat) -> R-C=O-CH2-COOH
    • Beta-keto-acid decarboxylation: -> R-COH=CH2 + CO2
    • Tautomerism: enol (above) -> R-C=O-CH3 (Keto)
  56. Acetoacetic ester synthesis (condensation)
    • Acetate: H3C-COO-
    • Acetoacetate: H3C-C=O-CH2-COO-
    • Ethylacetate: H3C-C=O-OEt abstract acidic H+ by base -> H2C=COH-OEt resonates to H2C--C=O-OEt which reacts with ethylacetate (carbanion attacks electrophillic ester C) to displace OEt -> H3C-C=O-CH2-C=O-OEt
    • You can use acetoacetic ester to make C-C bonds: H3C-C=O-CH2-C=O-OEt + R-X (R- substitutes on to CH2 in between 2 carbonyls); hydrolysis removes EtOH to make H3C-C=O-CRH-COOH; decarboxylation -> H3C-C=O-CH2-R + CO2
  57. Amines: Nomenclature, Stereochemistry, Physical Properties
    • Nomenclature: prefix amino- (ex. 2-amino propanoic acid) or suffix -amine (ex. propanamine)
    • Stereochemistry: tertiary amines can be chiral but always racemic due to spontaneous inversions at room temp, quaternary amines stay chiral (no inversions)
    • IR: primary R-NH2 = 2 N-H = 2 peaks ~3300; secondary R-NH-R' = 1 N-H = 1 peak ~3300; tertiary R3N = no N-H = no peak @ 3300
  58. Amide formation (peptide bond)
    • Amine + acid (or derivative with a good leaving group) -> amide
    • R-COOH + H2N-R' -> R-C=O-NH-R'
  59. Aromatic amine reacts with nitrous acid
    • Ar-NH2 + HONO -> Ar-N2+ + H2O + OH-
    • * N's are triple bonded, + is localized near the aromatic ring due to 4th bond
  60. Alkylation of an Amine (or polyalkylation)
    • R-CH2-X + H2N-R' (+ base) -> R'-NH-R + HX
    • Polyalkylation can add 2 or even 3 (making 4 bonds and a positive charge)
  61. Hofmann Elimination and Amines
    • Amine + Methyl iodide -> exhaustive methylation of the amine (3 Me and a positive charge) -> fully methylated amine is a good leaving group
    • 2-amino butane + MeI -> 2-(N(Me)3)-butane -> 1-butene
  62. Amines: General Principles
    • Basic: like to gain a proton, difficult for neutral amines to lose a proton, amides can lose a proton b/c carbonyl contributes to a resonance structure that places the negative on oxygen
    • Stabilize adjacent carbocations: donates its lone pair to adjacent carbocation
    • Substituents: aromatic amines with e- donating groups (e.g. -OH) are even more basic, Ar-NH2 with e- withdrawing groups (e.g. NO2 +) are less basic, steric effectscan reduce basicity because protonated amines are bigger which increases steric interactions, aromatic amines are weaker bases than aliphatic
Card Set:
MCAT Organic Chemistry
2014-05-06 19:20:18
OChem MCAT Science Organic Chemistry

Everything that would reasonably fit in a card set on naming organic compounds, stereochemistry, and the important reactions of different species (no diagrams)
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