3. Lab techniques

Question 1

How do you extract organic amines?

Answer 1

amines are bases. To extract these, we add a dilute acid (e.g. 10% HCl).

the base (electron donating) attacks the acid, deprotonating it. The resulting cationic salt is freely soluble in aqueous solution.

Question 2

How do you extract carboxylic acids?

Answer 2

To extract a carboxylic acid, we use a dilute base (10% NaHCO3). The base attacks and deprotonates the acid. the resulting anionic salt is freely soluble in aqueous solution.

Question 3

How do we extract phenols?

Answer 3

phenol is quite stable and therefore, we need a stronger base. We use NaOH. NaOH may also be used for carboxylic acids.

Question 4

How do we separate an organic solution that contains an strong acid, a weak acid, and a weak base?

Answer 4

1. We use a weak base like sodium bicarbonate (NaHCO3) to pull out the strong acid. This won’t be strong enough to react with the weak acid (nor will a base react with a base)
2. We can either use a strong acid (HCl) to pull out the weak base. Or we can use a strong base (NaOH) to pull out the weak acid.

pull out = pull into the aqueous solution, from the organic phase.

Question 5

Thin layer chromatography: What does it separate? mobile vs stationary phase?

Answer 5

TLC separates organic compounds based on their polarity. The stationary phase is a POLAR surface. The mobile phase is a NON-polar solvent that travels up the silicon slide.

More polar molecules interact with the stationary phase and do not travel far. Non-polar molecules get carried up with the non-polar solvent (mobile phase).

Question 6

TLC: What is an Rf value?

Answer 6

The Rf value is the distance traveled by a given compound divided by the distance traveled by the non-polar solvent

Rf is always positive, never greater than 1

Question 7

TLC: what kind of molecules does it separate?

Answer 7

small molecules that typically have high MPs and BPs

Question 8

Column (flash) chromatography: What does it separate? mobile vs stationary phase?

Answer 8

Same as TLC, separates molecules based on polarity. UNLIKE TLC, column chromatography is used for bulky compounds.

non-polar solvent is poored into the top of the column. Non-polar molecules will be dragged down with it and elute first. POLAR compounds will interact with the stationary polar phase and elute last.

Question 9

Ion Exchange Chromatography: What does it separate? mobile vs stationary phase?

Answer 9

Separates compounds based on charge. Most frequently used with amino acids or entire proteins.

stationary phase: a charged resin
mobile phase: the analyte which contains negative and positive molecules.

Question 10

What is a cationic exchange resin?

Answer 10

A cationic exchange resin means that the separation funnel is fixed with a negatively charged species that is associating with some positive ion (e.g. SO3- is fixed to the funnel and Na+ is interacting with it).

When the analyte is poured in, the positive ions displace Na+ and bind the negative resin (hence, cationic exchange). Thus neutral and anionic species elute first. After, Na+ can be poured through to displace the cation and allow to elute.

an anionic exchange resin would be the opposite

Question 11

What is high pressure liquid chromatography (HPLC)? What is reverse phase HPLC?

Answer 11

HPLC is the same as column chromatography but uses pressure to force the mobile phase to move faster. Here, the polar stationary phase holds polar molecules, while non-polar molecules elute first.

reverse-phase HPLC: the stationary phase is NON-POLAR. Thus, polar molecules elute first.

Question 12

Size Exclusion Chromatography: What does it separate? mobile vs stationary phase?

Answer 12

Size exclusion chromatography is used to separate bulky compounds of varying size.

stationary phase: inert polymer beads that slow down small molecules
mobile phase: analyte of interest

Question 13

Explain the elution pattern of Size Exclusion Chromatography.

Answer 13

The inert beads of the stationary phase interact with small molecules. SO, large molecules elute first while smaller molecules elute last.

Question 14

When can a size exclusion separation fail?

Answer 14

Sometimes the shape of the compounds can be odd (a thin oval). Thus in 1D, the molecule may fit into the pours, despite it being a large molecule.

We can cross-reference the results of an SDS page to see this (separates based on molecular weight)

Question 15

Affinity Chromatography: What does it separate? how does it work (4 steps)?

Answer 15

Affinity chromatography is more applicable to medical examples, separating complex cell lysates or blood samples.

1. Add an antibody to the solution that is highly specific for the protein of interest (call it antigen)
2. We add another protein that is highly specific for the already added antibody.
3. centrifugation. the heavy protein-antibody-antigen complex goes to bottom
4. drain the supernatant

instead of centrifugation, we can also use magnetic beads as the solid phase. We then isolate these beads using a magnet.

Question 16

Gas Chromatography: What does it separate? mobile vs stationary phase?

Answer 16

used to separate molecules with varying volatilities. In particular, low BP molecules.

We heat up a stationary phase liquid solution. As molecules evaporate into the air, they contact an inert gas mobile phase which drags them to some detector. This detetcs the molecules and reports their identity and quantity.

Question 17

Gas Chromatography: What is the elution pattern?

Answer 17

Molecules that evaporate more easily, (low BPs, high VPs) will elute first.

Question 18

What are the two biggest factors that determine the melting and boiling points of hydrocarbons (in order)?

Answer 18

1. Branching: more highly branched compounds cannot compact as easily and thus, experience reduced dispersion forces.
   - a more branched compound will have a lower BP and MP
2. Molecular weight: heavier hydrocarbons have more surface area for dispersion forces. Thus, heavier molecules will have higher BP and MP.

Question 19

t or f for unbranched hydrocarbons at standard conditions…
1-4 carbons = gas
5-16 = liquid
16+ = solid

Answer 19

True! This is because of their MW. Heavier hydrocarbons have increased dispersion forces are less likely to evaporate.

branching will change these results.

Question 20

How does hydrogen bonding effect the physical properties of organic compounds (n=2)?

Answer 20

1. Intermolecular H-bonds are very strong. Many of the same molecule can H-bond, the BP and MP will be high
2. Intramoleclar H-bonds will REDUCE the BP and MP. This is because if a molecule H-bonds to itself, then it cannot H-bond with its other members in solution.

compare 4-nitrophenol with 2-nitrophenol, the latter can intramolecular H-bond.

Question 21

t or f, despite intramolecular bonding, molecules with H-bonding components will have higher BPs than ones that do not.

Answer 21

true for most cases.

Question 22

What is a distillation?

Answer 22

Process of increasing the temperature of an organic solution until a member of the solution can overcome its IMFs that hold it in a liquid phase. (i.e. separation based on BP)

the vapor rises up and the condenses in a separate column.

Question 23

What is the difference between a simple distillation and a fractional distillation?

Answer 23

Simple –> used to remove impurities or to separate compounds with very different boiling points.

fractional (uses longer funnel with a condensation material) –> used to separate compounds that have boiling points within 20 degrees.

Question 24

What is absorption spectroscopy in general?

Answer 24

Absorption spectroscopy involves exposing molecules to light energy so they enter an excited state. You then measure the energy released when the molecules return to their ground state. This can be unique for certain compounds.

Question 25

What is mass spectroscopy? How does it work?

Answer 25

Mass spectroscopy is used to determine the mass of compounds in a sample. High energy electrons bombard a sample and cause it to ionize. The ionized molecules pass a magnetic field and their flight path indicates their mass.

Question 26

Mass spectroscopy: On an abundance vs M/e graph, explain why their are multiple peaks of varying heights.

Answer 26

1. multiple peaks: the ionizing electrons can break certain molecules. So some smaller peaks can have smaller M/e values. If an M/e value is greater than the mass of the molecule its is caused by an isotope.
2. the height of the peaks represents the abundance of molecules.

Question 27

What is UV / Vis spectroscopy? What is it used for?

Answer 27

A form of absorption spectroscopy used to identify highly conjugated organic compounds.

Question 28

UV / Vis spectroscopy: the maximum wavelength absorbed by a conjugated system is determined by what?

Answer 28

The longer the conjugated system, the higher wavelength it absorbs.

Note: using a color wheel, the conjugated system will appear whatever is opposite to what it absorbs.

absorbs 625 nm = orange light. Therefore, it appears blue which is opposite orange.

Question 29

Explain the order of the electromagnetic spectrum.

Answer 29

radio IR ROYGBIV UV x-ray gamma-ray

decreasing wavelength –>

Question 30

What is IR spectroscopy?

Answer 30

IR radiation makes covalent bonds vibrate at specific frequencies. Knowing these frequencies or wave-numbers (1 / wavelength) we can determine the composition of a compound.

Question 31

IR spectroscopy: In cm-1, what are the stretching frequencies for…

1. Alcohols (O-H)
2. Carbonyls (COOH)
3. Alkenes
4. Alkynes

Answer 31

1. Alcohols (O-H) –> 3600 - 3200
2. Carbonyls (C=O) –> 1700
3. Alkenes –> 1650
4. Alkynes –> 2200

Question 32

IR spectroscopy: Compare alcohols and carbonyls in terms of the shape of their peaks.

Answer 32

alcohols = broad and strong (3400)
carbonyls = sharp (intense) and strong (1700)

Question 33

Where is the CH stretch in IR spectroscopy?

Answer 33

The CH stretch is also near the 3200 range (like alcohols), however, it is sharper whereas OH groups are broad.

sp CH = 3300
sp3 CH = 2900

Question 34

NMR spectroscopy: What are equivalent hydrogen’s?

Answer 34

Equivalent hydrogen’s are H atoms with identical electronic environments. For every set of equivalent H’s, there is 1 NMR signal.

in propane, there are two sets of equivalent hydrogen’s and therefore two signals.

Question 35

NMR spectroscopy: What is splitting?

Answer 35

A proton (H) with n-neighboring non-equivalent hydrogen’s, it will have n+1 peaks in its respective signal.

in propane, the center carbon has two H’s. These H’s have 6 non-equivalent hydrogen neighbors. Therefore, they have a 7-peaked signal.

Question 36

NMR: What is a singlet, doublet, and triplet?

Answer 36

singlet: spliting = 1 , no non-equivalent hydrogen’s (splitting = 0 + 1)
doublet: splitting = 2, one non-equivalent H (1 + 1 = 2)

etc.

Question 37

If we were to look at a NMR spectrum, what does the number of resonances tell us?

Answer 37

The number of sets of equivalent hydrogen’s. Resonance = signals.

Question 38

Fill in the gaps: Protons that are more deshielded will be more _____ (at ___ ppm). Protons that are more shielded will be more ____ (at ___ ppm).

Answer 38

Protons that are more deshielded will be more downfield / left (at higher ppm). Protons that are more shielded will be more upfield / right (at lower ppm).

Question 39

How can we determine if a proton is shielded or desheilded?

Answer 39

More electrons = more shielding

protons near electronegative atoms are de-shielded since the EN atom pulls electrons away. Protons near electron-donating groups will be shielded.

Question 40

how does hybridization effect shielding in NMR?

Answer 40

the greater the s-character, the more deshielding. Since p-orbitals contribute to electron density.