MASTER CHEM221 FINAL

Hydroxyl Group

A functional group characterized by a hydrogen atom bonded to an oxygen atom, commonly found in alcohols.

Amine

A functional group consisting of a nitrogen atom bonded to 3 other atoms (C or H)

Nitrile

carbon triple-bonded to nitrogen

Alkene

A functional group characterized by at least one carbon-carbon double bond

Alkyne

A functional group characterized by at least one carbon-carbon triple bond

Arene

a functional group that's an aromatic ring with carbon-carbon double bonds

Halide

Carbon bonded to a halogen (Br, Cl, F, I)

Alcohol

Carbon bonded to an OH (R-OH)

Ether

2 carbons bonded to an O on either side (R-O-R)

Primary carbon

a carbon bonded to only one other carbon

Secondary carbon

carbon bonded to two other carbons

Tertiary carbon

carbon bonded to three other carbons

methyl carbon

carbon attached to 3 hydrogens

Alkanes

C--C and C--H bonds

Aldehyde

type of carbonyl FG

C double bonded to O and single bonded to H

Ketone

type of carbonyl FG

3 carbons single bonded to each other, with the middle double bonded to an O

Amide

type of carbonyl FG

Carbon single bonded to N and double bonded to O

carboxylic acid

type of carbonyl FG

carbon double bonded to O, single bonded to OH

Ester

type of carbonyl FG

C double bonded to O, single bonded to O-C

Alkyl Group

A group of carbon and hydrogen atoms derived from alkanes by removing one hydrogen atom.

Ethyl Group

An alkyl group containing two carbon atoms and five hydrogen atoms, represented as -C2H5

Et-

Propyl Group

An alkyl group with three carbon atoms and seven hydrogen atoms, represented as -C3H7.

Pr-

Butyl Group

An alkyl group made up of four carbon atoms and nine hydrogen atoms, represented as -C4H9.

Bu-

Isopropyl Group

A branched alkyl group derived from propane, with the structure -C3H7, where the central carbon is connected to two other carbons.

iPr-

Tert-Butyl Group

A branched alkyl group consisting of four carbon atoms, with the structure -C4H9, where three methyl groups are attached to a central carbon.

tBu-

Pentyl

alkyl group made up of 5 carbons

Pe-

Hexyl

alkyl group made up of 6 carbons

Hex-

Heptyl

alkyl group made up of 7 carbons

Hep-

Octyl

alkyl group made up of 8 carbons

eclipsed

when the atoms are blocking each other from the frontal view

staggered

when all atoms are visible from the frontal view

anti

when the atoms are in opposite positions of each other

(the 2 X’s)

syn

when the atoms are in the same position

(the 2 X’s)

gauche confirmation

This is one of the four conformations seen in a Newman projection. This confirmation occurs when the largest substituents are 60° apart from one another. This is the second-most stable confirmation.

Chair confirmation

Most stable confirmation of cyclohexane

Cis orientation

2 high bonds OR 2 low bonds

(ex. Ha on C1 and He on C2 OR He on C1 and Ha on C2

Trans orientation

1 high bond and 1 low bond

(ex. He on C1 and He on C2 OR Ha on C1 and Ha on C2)

isomer

same formula different structure

constitutional isomer

differs by atom connectivity

stereoisomer

different in arrangement of atoms in 3D space

superimposable

to align all parts/atoms perfectly overlapping two objects such that they match exactly in three-dimensional space.

IDENTICAL

nonsuperimposable

2 mirror image molecules that can’t be placed on top of each other to align perfectly in 3D space

chiralty

hardedness

chiral

mirror image is non-superimposable

achiral

mirror image is superimposable (bottom part of pic)

chiral center

a tetrahedral (-like, sp3) atom (C) with 4 different groups attached

enantiomers

stereoisomers that are non-superimposable mirror images

racemic mixture

1:1 mixture of enantiomer

diastereomer

any stereoisomers that are not an enantiomer (not superimposable, not mirror images

meso compound

An achiral molecule that contains 2 or more chiral centers, but has an internal mirror plane

R & S Nomenclature for chiral centers

1. assign priority to each atom attached to the chiral center

   1. higher atomic # → higher priority

   2. highest priority #1, lowest #4

   3. I > Br > Cl > S > F > O > N > C > H

2. if no difference at the first attached atom, move along the chain until there is a difference

   1. multiple bonded atoms are equivalent to the same number of single bonds

3. orient the molecule so the lowest priority group (#4) is in the back

4. starting with the highest priority #1, move to #2, then #3

   1. clockwise → R

   2. counterclockwise → S

Possible Structures (of elimination products, lab 7)

looking at the double bonds:

1. trans

2. cis

3. terminal

MS (mass spectrometry)

1. ionize sample

2. separate and detect mass of ion [and its fragments]

• detects “+” charged ions/fragments by mass (unit is M/Z)

• Br detection:

  • 1:1 M ratio → [M]+ contains Br⁷⁹, and [M]2+ contains Br⁸¹

• Cl detection:

  • 3:1 ratio → [M]+ contains Cl³⁵, and [M]2+ contains Cl³⁷

Infrared (IR) Spectroscopy

• IR causes molecular vibration if the energy is at the appropriate level (energy is reported in wave numbers, in units of cm-1)

• molecular vibrations depend on:

  • bond strength (of any given A—B bond); stronger bond, the more E it takes to move atoms ( higher E, higher wave numbers)

  • atom size; larger atom, lower wave number

• things to look out:

1. C=O stretch (1780-1630cm-1)

   1. O—H stretch (3400-2400) → carboxylic acid

   2. N—H stretch (3500-3100) → amide

   3. C—H stretch (2700-2800) → aldehyde

   4. none → ketone or ester

2. C—H stretch

   1. <3000 (sp³ C—H)

   2. >3000 (sp² [alkyne or arene] or sp C—H [alkyne])

3. Broad O—H stretch

   1. 3500-3200: alcohol

   2. 3400-2400 + carbonyl stretch

4. sharp N—H stretches (3500-3100)

   1. 2 bands= R—NH₂ or R—C=O NH2

   2. 1 band= RNHR or RC=O NHR

5. triple bonds (2300-2100)

   1. C triple bond C (2150) → alkyne

   2. C triple bond N (2250

Intermolecular Forces

• London dispersion forces (weak)

  • larger the mass, more the dispersion force, higher bp

  • more linear the structure, more the dispersion force, higher bp

• dipole-dipole interaction (medium)

  • polar moelcules align according to the direction of their net dipole moments

• hydrogen bonds (strong)

  • special type of dipole-dipole interaction involved H-atom and EN atoms

Lab 1- Aqueous Organic Extraction and recrystallization

• 2 solvents separate based on density (for this, it’s ethanol solution on top, water on bottom)

• desired product is in aqueous layer (H2O), so it can be drained out

• for this lab (based on exam 1 question), the following is correct:

  • top layer is aqueous HCI

  • after HCI addition, the species in the top layer is CH3(CH2)3NH2

  • bottom layer is dichloromethane (organic solvent)

  • after HCl addition, the species in the bottom layer is pentane

Lab 2- Distillation and Boiling Point

• Compound that will be collected last is the one with a more stable structure. determine this with its ability to form hydrogen bonds with other molecules (lone pairs), maybe resonance, etc.

• Blue section: where the compound is being condensed, going from a vapor to a liquid (using water), and then being collected in the tube

• for boiling point:

  • the larger the mass, the more dispersion force, the higher the boiling point

    • london dispersion force- depends on size and shape

  • the more linear the structure, the more dispersion force, the higher the boiling point

Labs 5, 6, 10- Reaction Kinetics and Mechanism

• image is for lab 5 specifically

• intermediates: look at what bonds are formed/broken (stepwise rxn)

• RDS: step with the highest TS

• kinetics: how fast the reaction is

  • rate= k * [reaction A]^a * [reactant B]^b etc…

  • k= rate constant, different for each rxn

  • [reactant X]= amount of reactants, usually in mole or M

  • a, b, ..= order (number of molecules involved in RDS)

Labs 1 and 8- Product melting point analysis

• purity of the isolated and dry solid can be estimated by recording its melting point on a melting point apparatus

• the compound can be identified by its melting point

  • can be confirmed by recording the melting point of a mixture of the isolated compound and an authentic sample of the compound (a mixed melting point)

• if the melting point of the mixture is the same as that recorded for the isolated compound, then the identity of the compound has been confirmed

Labs 7, 9, and 10- GC-MS

• mass spec- measure the m/z of the ion ([M]+)

GC:

1. separate organic compounds based on volatile nature (~ boiling point)

2. the more volatile (~ lower BP) compounds reach the detector earlier, the less volatile the compounds later. time when the detector detects the compound is retention time (RT)

3. quantify of the compound = the “area-under-the-curve” of the peak

• MS provides spectrum of abundance vs mass of ions generated during the analysis of the compound

  • each compound will fragment in a pettern unique to that compound

• GC chromatogram: graph of abundance (total ion count) vs time (top of image)

  • RT of the peak identifies pure compounds

  • integration of each peak (area % of total) can be used to determine the relative percent composition of each compound in mixture

• Mass spectra: abundance vs mass (mass/charge ratio) (bottom of image)

  • each GC chromatogram peak will have a separate mass spectra

  • the likely molecular weight and fragmentation pattern can be used for product identification

Lab 11- Reflux setup, MS fragmentation

• molecular fragments: fragmentation gives the most stable carbocation/carbon radical

  • for this lab, either 1 degree alcohol or 2 degree alcohol as possible products

• reflux setup (image): condenser traps solvent vapors by cooling them and forcing the condensed solvent back into our rxn flask

  • observe rxn mixture to determine when the process of reflex starts (condensation around the side of the round bottom flask)

VSPER

• 4e- domain: tetrahedral-like

  • angle (tetrahedral)- 109 degrees

• 3e- domain: trigonal planar-like

  • angle (trigonal planar)- 120 degrees

• 2e- domain: linear angle 180 degrees

• double/triple bonds count as a 1e- group

Polarity of chemical bonds

• EN: ability of an atom to compete for e- with other atoms

  • quantified between 0.7 and 4.0 (figure will be on exam)

• less than 0.5 difference= nonpolar

• 0.5-2.0= polar

• 2.0+= ionic

resonance structure

• if a compound contains less than or equal to 2 RS, then none of the individual RS lewis structures represent the TRUE structure of the compound

  • true structure- hybrid of all of them

• best RS → closest to the true structure

• 2nd best RS → hints at reactivity of compoudn

valence bond theory

• atomic orbitals can undergo hybridization to generate hybrid orbitals

• # of hybrid oribtal = # of atomic orbitals combines for hybridization

• 2p orbitals are 90 degrees with respect to each other

• single bonds between atoms- sigma bond

• pz orbitals= double/triple bonds, which are pi bonds

  • double bond=1 pi bond (1 pz)

  • triple bond= 2 pi bonds (1 py and 1 pz)

Bronsted acid-base

• acid= any species that donates a proton (H)

• base= any species that accepts a proton

• equilibrium arrow- species on both sides of the equation are present

  • if equilibrium favors product/right side- strong acid, large K_a, and small/lower pK_a

  • if equilibrium favors reactant/left side- weak acid, small K_a, and large/higher pK_a

• general trends:

  • conjugate acid with higher pka gets the proton

  • stronger acid HA makes a weak base A-, and a weak acid HA makes a strong base A-

• examples:

  • acid- water, HCl

  • base- water, methoxide anion, azide anion

Strengths of different acids

The more stabilized A- is, the more willing HA is to give its H+

1. EN and induction effect

   1. looking at the row

   2. ex: F > O > N > C

   3. F- > OH- > NH2- > CH3-

   4. F > H

2. polarizability and size: large atoms can diffuse e- density over a larger atomic radius

   1. looking at column (comes first in determining stronger acid, ie I vs F)

   2. ex: I > Br > Cl > F (stability of I- > Br- > Cl- > F-)

   3. S > O / H3CS- > H3CO-

3. resonance: delocalization of ‘-’ charge and/or e- to more evenly share the “burden”

4. hybridization: higher % of s-character in hybrid orbital, then more stabilized e- density (sp3, sp2, sp)

Lewis Acid-Base reactions

• acid (LA): electron acceptor

  • e- deficient/poor → electrophile (E+)

• base (LB): electron donor

  • e- rich → Nucleophile (Nu)

• in general, this rxn involves formation of a new covalent bond

• all Bronsted acids/bases are Lewis acids/bases, BUT, not all lewis acids/bases are bronsted acids/bases

• examples:

  • LA- water, BF3, Na+, Trityl cation, HCl

  • LB- water, methoxide anion, azide anion

• strengths of acids and bases:

  • nucleophilicity- tendency of Nu to form a (covalent) bond with E+ (often trends qualitatively with the pKa of their conjugate bronsted acid)

  • electrophilicity- tendency of E+ to form a (covalent) bond with Nu

E1 reactions

• weak-moderate base

• good LG

• electrophile: 3 > 2

• polar solvent

• 1st order kinetics

• stereochemistry: E and Z isomers

• rearrangement common

• 2 steps

E2 reactions

• strong base (KOtBu, LDA, also heat)

• good LG

• 3 > 2 > 1

• polar solvent

• 2nd order kinetics

• stereochemistry: anti-coplanar geometry

• no rearrangement

• 1 step

SN1 reaction

• just needs any nucleophile

• good LG

• 3 > > 2 electrophile

• polar protic solvent good (water, ethanol)

• 1st order kinetics

• stereochemistry: racemic mixture

• common rearrangement

• 2 steps

SN2 reaction

• strong nucleophile needed

• good LG

• electrophile: methyl > 1 > 2

• polar aprotic solvent good (DMF, DMSO)

• 2nd order kinetics

• stereochemistry: inversion of configuration

• no rearrangement

• 1 step

Nucleophile properties

• anionic Nu stronger than neutral Nu (OH- stronger than H2O)

• periodic trends → nucleophilicity

  • increases right to left

    • more EN, worse Nu

    • less EN, good Nu

  • increases top to bottom

    • size and polarizability

LG properties

• e- withdrawing group, ie polarizable C—LG bond

• LG- needs to be stable on its own after it leaves, via resonance or polarizability

• common LGS: leave as anion (Cl-, Br-, etc.) OR neutral molecule (H2O, etc.)

• poor LG: OH, C—OH, OR-, NR2-, CH3-, H-, F-, etc.

Reaction Coordinate Diagram

analyzing the image:

• Pathway A vs Pathway B, 2 different products and 2 intermediates

• IB is lower in energy (more stable) than IA

• delta G_B is lower energy than delta G_A

• therefore, Pathway B is the faster and preferred rxn pathway, which forms the most stable and lowest energy intermediate

• transition state: high energy point where bonds are being formed/broken (NOT INTERMEDIATE)

• thermochemistry: delta G ~ delta H

  • if delta H < 0, rxn is exothermic/favorable

  • if delta H > 0, rxn is endothermic/not favorable

Stabilizing Carbon reactive intermediates

1. resonance: donation of e- density from adjacent lp or pi bond

2. hyperconjugation: donation of e- from adjacent sigma bonds (sigma bonds adjacent to empty p-orbitals can share e- density)

   1. 3 > 2 > 1 > methyl (most hyperconjugation → least hyperconjugation AND most stable intermediate → least stable intermediate

3. free radical substitution reactions

substitution reactions

1. one-step sub rxn (concerted)

   1. RDS: only one step - A—B C- → A- B—C

   2. rate law: rate= k[A—B]¹ * [C-]¹

   3. total order: 2, 2nd order

2. multi-step sub rxn (stepwise)

   1. A—B C- → A- B+ C- → A- B—C

   2. scenario 1: Step 1 is RDS

      1. rate= k[A—B]¹

      2. total order: 1

   3. scenario 2: step 2 is RDS

      1. rate= k[B+]¹ [C-]¹

      2. total order: 2

Addition reactions

1. syn addition (X—Y added at same time)

2. anti addition (X—Y added diff time through intermediate bridge)

3. random addition (X—Y added at dff time through planar intermediate [C cation or radical])

Markovnikov’s Rule

• when H—A is added to C==C, the H+ adds to the least substituted carbon (carbon with the most H)

• C with most H gets 1 more H