Organic Chemistry Flashcards
Carboxylic acid
Prefix: carboxy-
Suffix: -oic acid
Anhydrides
Prefix: alkanoyloxy- and carbonyl-
Suffix: anhydride
Esters
Prefix: alkoxycarbonyl-
Suffix: -oate
Amides
Prefix: carbomoyl-
Suffix: -amide
Aldehydes
Prefix: oxo-
Suffix: -al
Ketones
Prefix: oxo- or keto-
Suffix: -one
Alcohols
Prefix: hydroxy-
Suffix: -ol
Single bond order
Bond type: σ
Hybridization: sp^3
Angles: 109.5
Example: C-C
Double bond order
Bond type: σ and π
Hybridization: sp^2
Angles: 120
Example: C=C
Triple bond order
Bond type: σ and 2π
Hybridization: sp
Angles: 180
Example: C≡C
Flow chart of isomers
- Same connectivity?
Yes - stereoisomers
No - structural - Require bond breaking to interconvert?
Yes - configurational (optical)
No - conformational - Nonsuperimposable mirror images?
Yes - enantiomers (non-superimposable mirror images; have opposite stereochemistry at every chiral C, same chemical and physical properties except for rotation of plane-polarized light and reactions in a chiral environment)
No - diastereomers (non-mirror-image stereoisomers; differ at some, but not all, chiral centers; different chemical/physical properties
Conformational isomers
Differ by rotation around a single sigma bond
- Staggered conformations have groups 60 apart; anti = largest groups are 180 and gauche = 60 apart
- Eclipsed conformations have groups directly in front of each other; totally eclipsed = largest groups are directly in front of each other; strain is maximized
SN1
- 2 steps
- Favored in polar protic solvents
- 3 > 2 > 1 > methyl
- Rate = k[RL]
- Racemic products
- Strong nucleophile not required
SN2
- 1 step
- Favored in polar aprotic solvents
- Methyl > 1 > 2 > 3
- Rate = k[Nu][RL]
- Optically active and inverted products
- Favored with strong nucleophile
Nucleophile
= “nucleus-loving”; tend to have lone pairs or π bonds that can form new bonds to electrophiles. Nucleophilicity is increased by increasing electron density
Nucleophilicity is determined by four major factors
- Charge: nucleophilicity increases with increasing e density (more negative charge)
- Electronegativity: nucleophilicity decreases as electronegativity increases because these atoms are less likely to share e density
- Steric hindrance: bulkier molecules are less nucleophilic
- Solvent: protic solvents can inhibit nucleophilicity by protonating the nucleophile or through H-bonding
In aprotic solvents:
F- > Cl- > Br- > I-
- Opposite in protic
Electrophile
= “electron-loving”; tend to have a positive charge or positively polarized atom that accepts an e pair from a nucleophile; electrophilicity is increased by increasing the positive charge
Most common: carbonyl carbons, substrate carbon in an alkane, carbocations
Leaving groups
Molecular fragments that retain the e after heterolysis (breaking a bond, with both e being given to one of the two products); the best LG will be able to stabilize extra e
Most common: weak bases, large groups with resonance, and large groups with e-withdrawing atoms
Cyclic strain
Angle strain: stretch or compress angles from normal size
Torsional strain: from eclipsing conformations
Nonbonded strain: from interactions wth substituents on nonadjacent carbons ; in cyclohexane, the largest substituent usually takes equatorial position to reduce nonbonded strain
Absolute configuration
An alkene is (Z) if the highest-priority substituents are on the same side of the double bond, and (E) if on opposite sides
- A stereocenter’s configuration is determined by putting the lowest-priority group in the back and drawing a circle from group 1 to 2 to 3 in descending priority
- If this circle is clockwise = R, counterclockweise = S
Alcohols
- Higher B.P. than alkanes due to H-bonding
- Weakly acidic hydroxyl hydrogen
Synthesis: - Addition of water to double bonds
- SN1 and SN2 rxns
- Reduction of carboxylic acids, aldehydes, ketones, and esters
- Aldehydes and ketones with NaBH4 or LiAlH4
- Esters and carboxylic acids with LiAlH4
Organic oxidation-reduction
Level 0: (no bonds to heteroatom): alkanes
Level 1: alcohols, alkyl halides, amines
Level 2: aldehydes, ketones, imines
Level 3: carboxylic acids, anhydrides, esters, amides
Level 4: (four bonds to heteroatom): carbon dioxide
Oxidation
Loss of electrons, fewer bonds to hydrogens, more bonds to heteroatoms (O, N, halogens)
Reduction
Gain of electrons, more bonds to hydrogens, fewer bonds to heteroatoms
Oxidizing agents
Good oxidizing agents have a high affinity for electrons (such as O2, O3, and Cl2) or unusually high oxidation states (like Mn7+ in permanganate, MnO4-, and Cr6+ in. chromate, CrO4^2-)
Reducing agents
Good reducing agents include sodium, magnesium. aluminum, and zinc, which have low electronegative and ionization energies. Metal hydrides are also good reducing agents, like NaH, CaH2, LiAlH4, and NaBH4, because they contain the H- ion
Alcohols and reactivity
- Alcohols can be converted to mesylates or tosylates to make them better leaving groups for nucleophilic substitution rxns
- Mesylates (-SO3CH3) are derived from methanesulfonic acid
- Tosylates (-SO3C6H4CH3) are derived from toluenesulfonic acid
- Alcohols can be used as protecting groups for carbonyls, as reaction with a dialcohol forms an unreactive acetal. After other rxns, the protecting group can be removed with aqueous acid
Phenols
The hydrogen of the hydroxyl group of a phenol is particularly acidic because the oxygen-containing anion is resonance-stabilized by the ring
Quinones and hydroxyquinones
The treatment of phenols with oxidizing agents produces quinones
- These molecules can be further oxidized to form a class of molecules called hydroxyquinones; many hydroxyquinones have biological activity
Ubiquinone
Also called coenzyme Q and is a vital electron carrier associated with Complexes I, II, and II of the ETC
- Ubiquinone can be reduced to ubiquinol, which can later be reoxidized to ubiquinone; this is sometimes called the Q cycle
Aldehydes
The dipole moment of aldehydes causes an elevation of boiling point, but not as high as alcohols because there is no hydrogen bonding
Synthesis:
- Oxidation of primary alcohols
- Ozonolysis of alkenes
Reactions:
- Rxns of enols (Michael additions)
- Nucleophilic addition to carbonyl
- Aldol condensation
- Decarboxylation
Aldol condensation
An aldehyde acts as both a nucleophile (enol form) and an electrophile (keto form). One carbonyl forms an enolate, which attacks the other carbonyl; after the aldol is formed, a dehydration rxn results in an α,β-unsaturated carbonyl
Carboxylic acids
Carboxylic acids have pKa values around 4.5 due to resonance stabilization of the conjugate base; electronegative atoms increase acidity with inductive effects; B.P. is higher than alcohols because of the ability to form two H-bonds
Synthesis:
- Oxidation of primary alcohols with KMnO4
Reactions:
- Formation of soap by reacting carboxylic acids with NaOH; arrange in micelles
- Nucleophilic acyl substitution
- Decarboxylation
Lactams
Cyclic amides are called lactase; these are named according to the carbon atom bonded to the nitrogen: β-lactams contain a bond between the β-carbon and the nitrogen, γ-lactams contain a bond between the γ-carbon and the nitrogen, and so forth
Lactones
Cyclic esters are called lactones; these are named not only based on the carbon bonded to the oxygen, but also the length of the carbon chain itself
Carboxylic acid derivatives
Contain three bonds to heteroatoms (O, N, halides, and so forth); as such, they can be interconverted through nucleophilic acyl substitution by swapping leaving groups
- Carboxylic acid derivatives can be ranked based on descending reactivity: (1) acyl halides are the most reactive (2) anhydrides (3) carboxylic acids and esters (4) amides are the least reactive
- A rxn that proceeds down the order of reactivity can occur spontaneously by nucleophilic acyl substitution
- A rxn that proceeds up the order of reactivity requires special catalysts and specific rxn conditions
Anyhydrides
- Synthesis via dehydration of two carboxylic acids
- Intramolecular formation of cyclic anhydride
Amides
- Formation from an anhydride
- Formation from an ester
- Hydrolysis (requires acid)
- Reduction to an amine
Esters
- Transesterification
- Hydrolysis
- Reduction
- Saponification
Strecker synthesis
Reagents: aldehyde, ammonium chloride (NH4Cl), potassium cyanide (KCN)
Gabriel (Malonic-Ester) synthesis
Reagents: potassium phthalimide, diethyl bromomalonate
Phosphoric acid
Is a phosphate group or inorganic phosphate (Pi); at physiological pH, inorganic phosphate includes both hydrogen phosphate (HPO4^2-) and dihydrogen phosphate (H2PO4-)
Pyrophosphate (PPi)
Is P2O7^4-, which is released during the formation of phosphodiester bonds in DNA; pyrophosphate is unstable in aqueous solutions, and is hydrolyzed to form two molecules of inorganic phosphate
Organic phosphates
Nucleotides with phosphate groups, such as ATP, GTP, and those in DNA
Extraction
Separates dissolved substances based on differential solubility in aqueous vs. organic solvents; uses a separatory funnel
Filtration
Separates solids from liquids
Chromatography
Uses a stationary phase and a mobile phase to separate compounds based on polarity and/or size
Distillation
Separates liquids based on B.P., which depends on intermolecular forces
Simple distillation
Can be used to separate two liquids with B.P. below 150C and at least 25C apart
Vacuum distillation
Should be used when a liquid to be distilled has a B.P. above 150C; to prevent degradation of the product, the incident pressure is lowered, thereby lowering the B.P.
Fractional distillation
Should be used when two liquids have B.P. less than 25C apart; by introducing a fractionation column, the sample boils and refluxes back down over a larger surface area, improving the purity of the distillate
Recrystallization
Separates solids based on differential solubility in varying temperatures
Electrophoresis
Used to separate biological macromolecules based on size and/or charge
Thin-layer or paper chromatography
Mobile phase: nonpolar solvent
Stationary phase: polar card
Common use: identify a sample
Reverse-phase chromatography
Mobile phase: polar solvent
Stationary phase: nonpolar card
Common use: identify a sample
Column chromatography
Mobile phase: nonpolar solvent
Stationary phase: polar gel or powder
Common use: separate a sample into components
Ion-exchange chromatography
Mobile phase: nonpolar solvent
Stationary phase: charged beads in column
Common use: separate components by charge
Size-exclusion chromatography
Mobile phase: nonpolar solvent
Stationary phase: polar, porous beads in column
Common use: separate components by size
Affinity chromatography
Mobile phase: nonpolar solvent
Stationary phase: beads coated with antibody or receptor for a target molecule
Common use: purify a molecule (usually a protein) of interest
Gas (GC) chromatography
Mobile phase: inert gas
Stationary phase: crushed metal or polymer
Common use: separate vaporizable compounds
High-performance liquid (HPLC)
Mobile phase: nonpolar solvent
Stationary phase: small column with concentration gradient
Common use: similar to column, but more precise
IR - alcohols
Wavenumber: 3100 - 3500 cm-1
Vibration: O-H (broad)
IR - ketones
Wavenumber: 1700 - 1750 cm-1
Vibration: C=O
IR - aldehydes
Wavenumber: 2700 - 2900 cm-1or 1700 - 1750
Vibration: (O)C-H or C=O
IR - carboxylic acids
Wavenumber: 1700 - 1750 cm-1 or 2800 - 3200
Vibration: C=O or O-H (broad)
IR - amines
Wavenumber: 3100 - 3500 cm-1
Vibration: N-H (sharp)
1H-NMR - RCH3
0.9
1H-NMR - RCH2
1.25
1H-NMR - R3CH
1.5
1H-NMR - CH=CH
4.6 - 6
1H-NMR - C=CH
2 - 3
1H-NMR - Ar-H
6 - 8.5
1H-NMR - CHX
2 - 4.5
1H-NMR - CHOH/CHOR
3.4 - 4
1H-NMR - RCHO
9 - 10
1H-NMR - RCHOCO-
2 - 2.5
1H-NMR - CHCOOH/CHCOOR
2 - 2.6
1H-NMR - CHOH-CH2OH
1 - 5.5
1H-NMR - ArOH
4 - 12
1H-NMR - COOH
10.5 - 12
1H-NMR - NH2
1 - 5
When analyzing NMR, look for:
- Types of protons: corresponds to the number of peaks seen in the spectrum
- Position of peaks: the further left-shifted (downfield) the peak, the more deshielded the proton; usually this corresponds to more electron-withdrawing groups
- Integration of peaks: the larger the integration, the more protons contained under the peak
- Splitting: hydrogens on adjacent carbons will split a peak into n + 1 subpeaks, where n is the number of hydrogens on the adjacent carbon
When analyzing NMR, look for:
- Types of protons: corresponds to the number of peaks seen in the spectrum
- Position of peaks: the further left-shifted (downfield) the peak, the more deshielded the proton; usually this corresponds to more electron-withdrawing groups
- Integration of peaks: the larger the integration, the more protons contained under the peak
- Splitting: hydrogens on adjacent carbons will split a peak into n + 1 subpeaks, where n is the number of hydrogens on the adjacent carbon
UV spectroscopy
Involved passing UV light through a chemical sample and plotting absorbance vs. wavelength; it is most useful for studying compounds containing double bonds and heteroatoms with lone pairs
