proteins- janice smith Flashcards
1
Q
What Are α-Amino Acids?
A
Definition: Naturally occurring amino acids have both an amino group (NH₂) and a carboxyl group (COOH) attached to the same carbon atom, known as the α-carbon.
Hence, they are called α-amino acids.
Side Chain (R group): This is the variable group attached to the α-carbon that determines the identity and properties of each amino acid.
2
Q
Proteins as Polyamides
A
Proteins are polyamides: long chains formed by joining amino acids through amide bonds (also known as peptide bonds).
A portion of a protein shows repeating units of amino acids linked by peptide bonds.
3
Q
General Features of α-Amino Acids
A
Number of Naturally Occurring Amino Acids: 20
Glycine is the simplest amino acid, where R = H. It is the only amino acid without a stereogenic (chiral) center.
All other amino acids (R ≠ H) are chiral due to the α-carbon having four different groups attached.
4
Q
Stereochemistry of amino acids
A
Chiral Center: All amino acids (except glycine) are chiral.
D and L system: Like sugars, amino acids are classified using D (right) and L (left) prefixes.
Naturally occurring amino acids in proteins are L-amino acids.
D-amino acids are rare in nature.
R/S Configuration: Based on CIP rules:
Most L-amino acids have S configuration.
Exception: Cysteine (due to the sulfur-containing side chain), which has R configuration despite being an L-amino acid.
5
Q
Naming Amino Acids
A
Amino acids have common names.
They can be represented by either:
A one-letter abbreviation, or
A three-letter abbreviation.
6
Q
What functional groups are attached to the α-carbon in an α-amino acid?
A
A: An amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom, and an R group (side chain).
7
Q
What makes glycine unique among amino acids?
A
A: Glycine has R = H and lacks a stereogenic center; it is not chiral.
8
Q
What are polyamides, and how are they related to amino acids?
A
A: Polyamides are chains formed by linking amino acids via amide (peptide) bonds, forming proteins.
9
Q
What is the side chain of an amino acid?
A
A: The R group attached to the α-carbon; it determines the amino acid’s identity and properties.
10
Q
How many naturally occurring amino acids are there?
A
20.
11
Q
What stereochemistry do naturally occurring amino acids have?
A
A: They are L-amino acids and most have the S configuration, except cysteine (which has R).
12
Q
Which amino acids are not chiral?
A
A: Glycine is the only one.
13
Q
What is the difference between D- and L-amino acids?
A
A: L-amino acids occur naturally in proteins; D-amino acids are rare and not commonly found in nature.
14
Q
How are amino acid names typically abbreviated?
A
A: Using either a one-letter or three-letter code.
15
Q
What structural feature defines an α-amino acid?
A
A: The amino group and carboxyl group are both attached to the same α-carbon.
16
Q
NEUTRAL AMINO ACIDS
A
These amino acids are classified as “neutral” because their side chains (R groups) are neither strongly acidic nor basic under physiological pH.
17
Q
ACIDIC AMINO ACIDS
A
These amino acids have carboxylic acid (-COOH) groups in their side chains that lose a proton (H⁺) at physiological pH (~7.4), making the side chains negatively charged (–COO⁻).
18
Q
BASIC AMINO ACIDS
A
These amino acids have basic (positively charged) side chains at physiological pH due to the presence of amine or imidazole groups.
19
Q
Amino Acid Classifications Recap
A
Acidic Amino Acids: Contain an additional –COOH group in the side chain
Examples: Aspartic acid, Glutamic acid
Basic Amino Acids: Contain an additional basic nitrogen atom
Examples: Lysine, Arginine, Histidine
Neutral Amino Acids: All others (hydrophobic, polar uncharged, etc.)
20
Q
Structural Exceptions and Stereochemistry
Proline
A
Unique because its nitrogen is part of a five-membered ring.
Unlike other amino acids that are primary amines, proline is a secondary amine (2°).
The ring structure restricts flexibility, often found in turns or kinks in protein chains.
21
Q
Isoleucine & Threonine
A
Each has two stereogenic centers: the α-carbon and an additional β-carbon.
This leads to 4 stereoisomers, but only one is found in proteins (L-isomer with specific configuration).
These are among the few amino acids that are diastereomers due to multiple chiral centers.
22
Q
Essential vs. Non-Essential Amino Acids
A
Humans can synthesize only 10 of the 20 standard amino acids.
The other 10 are essential amino acids — they must be obtained through the diet.
In diagrams like this, they are often marked with an asterisk (*).
23
Q
Which amino acid is a secondary amine, not a primary amine?
A
A: Proline – its nitrogen is part of a five-membered ring.
24
Q
Which two amino acids have two stereocenters?
A
A: Isoleucine and Threonine
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What makes proline structurally unique?
A: It forms a ring with the α-amino group, making it a 2° amine and limiting backbone flexibility.
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Why do isoleucine and threonine have four stereoisomers each?
A: They have two chiral centers (α and β carbons), allowing for 2² = 4 stereoisomers.
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Which amino acids are classified as acidic?
A: Aspartic acid and Glutamic acid
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Which amino acids are basic?
A: Lysine, Histidine, Arginine
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What determines if an amino acid is acidic or basic?
A: Presence of an extra –COOH group (acidic) or basic nitrogen group (basic) in the side chain.
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What are essential amino acids?
A: Amino acids that cannot be synthesized by the human body and must be obtained from food.
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How many essential amino acids are there?
A: 10
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Zwitterions: The Real Form of Amino Acids
Zwitterion: A molecule that has both a positive and a negative charge but is overall electrically neutral.
In aqueous solution (especially around pH ~7), amino acids exist as zwitterions, not in their "neutral" form.
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the zwitterion has:
A positive charge on the ammonium ion (–NH₃⁺)
A negative charge on the carboxylate ion (–COO⁻)
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➤ Functional Groups:
Amino group (–NH₂) acts as a base → accepts a proton → becomes –NH₃⁺.
Carboxylic acid group (–COOH) acts as an acid → donates a proton → becomes –COO⁻
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T/F The neutral structure (NH₂ and COOH) is theoretical and does not really exist in water.
True
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Physical Properties of Amino Acids
Since amino acids are ionic compounds (salts) in solution:
They have high melting points
They are highly water soluble
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pKa Values & Ionization
Each amino acid has at least two ionizable groups:
Carboxyl group (–COOH)
pKa ≈ 2
Amino group (–NH₃⁺)
pKa ≈ 9
🧬 At low pH (acidic): amino acid is fully protonated → net positive charge.
🧬 At high pH (basic): amino acid is deprotonated → net negative charge.
🧬 At pH ≈ 7: zwitterionic form dominates → net charge = 0.
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What is a zwitterion?
A: A molecule with both positive and negative charges but an overall neutral charge.
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At what pH do amino acids exist primarily as zwitterions?
A: At pH ≈ 7
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Which form of amino acid does not exist appreciably in water?
A: The uncharged, neutral form (with NH₂ and COOH).
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What is the typical pKa of the –COOH group in amino acids?
A: ~2
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What is the typical pKa of the –NH₃⁺ group in amino acids?
A: ~9
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What happens to an amino acid at pH below its isoelectric point?
A: It gains protons and becomes positively charged.
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What happens to an amino acid at pH above its isoelectric point?
A: It loses protons and becomes negatively charged.
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Why do amino acids have high melting points and water solubility?
A: Because they exist as ionic salts (zwitterions) in aqueous solution.
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Which amino acids have additional ionizable groups in their side chains?
A: Acidic amino acids (e.g., aspartic acid) and basic amino acids (e.g., lysine).
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How do side chains affect the acid–base behavior of amino acids?
A: They introduce additional pKa values and influence the molecule’s overall charge.
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Explanation: Amino Acid Charge vs. pH (Figure 28.3)
This figure illustrates the three ionization states of a neutral (non-ionizable side chain) amino acid as pH increases. The changes occur due to protonation or deprotonation of the amino and carboxyl groups.
🟢 At Low pH (≈ 2) — Fully Protonated
Structure:
Amino group: –NH₃⁺ (protonated, positively charged)
Carboxyl group: –COOH (protonated, neutral)
Net Charge: +1
Dominant species in acidic environments
Explanation: At low pH, H⁺ is abundant, so both functional groups are protonated.
⚪ At Neutral pH (≈ 7) — Zwitterion
Structure:
Amino group: –NH₃⁺ (still protonated)
Carboxyl group: –COO⁻ (deprotonated)
Net Charge: 0
Zwitterionic form
Explanation: Carboxylic acid (pKa ~2) loses H⁺, while amino group (pKa ~9) retains its proton.
🔵 At High pH (≈ 10) — Fully Deprotonated
Structure:
Amino group: –NH₂ (neutral, deprotonated)
Carboxyl group: –COO⁻ (still deprotonated)
Net Charge: –1
Dominant species in basic environments
Explanation: OH⁻ removes H⁺ from the ammonium group.
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What is the charge on a neutral amino acid at pH ~2?
+1, due to protonated NH₃⁺ and uncharged COOH
48
What is the net charge of a neutral amino acid at pH ~7?
A: 0 — it exists as a zwitterion
49
What is the charge at pH ~10?
A: –1, due to deprotonated COO⁻ and neutral NH₂
50
What happens to the carboxylic acid group as pH increases past 2?
A: It loses a proton, becoming –COO⁻
51
What happens to the amino group as pH increases past 9?
A: It loses a proton, becoming –NH₂
52
What is a zwitterion?
A molecule with both a positive (NH₃⁺) and a negative (COO⁻) charge, but an overall net charge of 0
53
Why is the zwitterion the dominant form at physiological pH?
A: Because it balances the ionization states of both the carboxyl and amino groups at pH ~7
54
What happens when a zwitterion is placed in a strong base like NaOH?
A: The NH₃⁺ group is deprotonated to NH₂, resulting in a net negative charge.
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When a zwitterion is placed in a strong base like NaOH, it loses a proton from the –NH₃⁺ group, becoming negatively charged (overall –1).
When a zwitterion (the neutral form of an amino acid at pH ≈ 7) is placed in a strong base like NaOH, the solution becomes basic, meaning it contains a high concentration of hydroxide ions (OH⁻). Here's what happens:
🔄 Deprotonation of the Amino Group
The ammonium group (–NH₃⁺) of the zwitterion loses a proton (H⁺) because the OH⁻ ions in NaOH pull off the H⁺.
This converts the –NH₃⁺ group into a neutral –NH₂ group.
🔋 Resulting Charge
The carboxyl group remains deprotonated (–COO⁻), as it already lost its proton around pH 2.
The amino acid now has:
–COO⁻ (negative charge)
–NH₂ (neutral)
➡️ Net Charge: –1
➡️ This is called the fully deprotonated form.
🧠 Summary in One Line:
When a zwitterion is placed in a strong base like NaOH, it loses a proton from the –NH₃⁺ group, becoming negatively charged (overall –1).
56
What happens to a zwitterion in a strong base like NaOH?
The –NH₃⁺ group loses a proton, converting to –NH₂, and the amino acid gains a net –1 charge.
57
What is the most direct method to synthesize an α-amino acid in the lab?
A: SN2 reaction of an α-halo acid with excess NH₃
58
What type of mechanism is used in this reaction?
A: Bimolecular nucleophilic substitution (SN2)
59
Why is a large excess of NH₃ used?
A: To drive the reaction to completion by ensuring full substitution of Br⁻
60
What functional group is introduced in the product of this reaction?
A: The amino group (–NH₂) at the α-carbon
61
What α-halo acid is used to synthesize valine?
A: α-bromoisovaleric acid: (CH₃)₂CH–CHBr–COOH
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Alkylation of Diethyl Malonate
Derivative (Amino Acid Synthesis)
The method shown in the image is a variation of the classic malonic ester synthesis, adapted to produce α-amino acids using diethyl acetamidomalonate. The advantage here is that the nitrogen needed for the amino group is already built into the starting material.
🔬 Overall Goal:
To synthesize an α-amino acid by attaching an alkyl group to the α-carbon of diethyl acetamidomalonate, then converting the molecule into the desired amino acid through hydrolysis and decarboxylation.
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Mechanism Summary:
Deprotonation (Enolate Formation):
NaOEt removes the acidic proton between the two carbonyls of diethyl acetamidomalonate, forming a stabilized enolate.
Alkylation:
The enolate attacks an alkyl halide (R–X), forming a new C–C bond. This is an SN2 reaction, so the alkyl halide must be primary/unhindered.
Hydrolysis and Decarboxylation:
Heating in acid converts esters to acids, and amides to amines. A decarboxylation (loss of CO₂) of the β-keto acid leads to the final α-amino acid. The nitrogen on the α-carbon is already present as part of the acetamide group.
This synthesis yields a racemic mixture of D- and L-amino acids (no stereoselectivity unless chirality is introduced).
Decarboxylation is facilitated because of the β-keto acid intermediate that’s unstable under heat.
64
What is the starting material in the alkylation of a diethyl malonate derivative for amino acid synthesis?
A: Diethyl acetamidomalonate.
65
What role does NaOEt play in the synthesis of α-amino acids from diethyl acetamidomalonate?
A: It deprotonates the α-hydrogen, forming a stabilized enolate.
66
What type of reaction is used to attach the R group to the enolate?
A: SN2 alkylation using an alkyl halide (R–X).
67
What happens during the final step of this synthesis when treated with H₃O⁺ and heat?
A: Hydrolysis of esters and amide occurs, followed by decarboxylation to yield the amino acid.
68
What functional group becomes the NH₂ group of the final amino acid?
A: The amide nitrogen on the α-carbon of the diethyl acetamidomalonate.
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Why does decarboxylation occur easily in this synthesis?
A: Because the intermediate is a β-keto acid, which is unstable and readily loses CO₂.
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Strecker Synthesis (Section 28.2C)
The Strecker synthesis is a classic method for preparing α-amino acids from aldehydes using a two-step reaction. It is particularly useful because it is simple, builds new C–C and C–N bonds, and works on a wide variety of substrates.
🧩 Overall Reaction Summary
General Steps:
Aldehyde + NH₄Cl + NaCN → α-Amino nitrile (RCH(NH₂)CN)
α-Amino nitrile + H₃O⁺ (acidic hydrolysis) → α-Amino acid (RCH(NH₂)COOH)
⚙️ Reaction Breakdown:
Step 1: Formation of α-Amino Nitrile
Ammonia (NH₃) adds to the aldehyde to form an imine.
Cyanide ion (CN⁻) attacks the imine carbon to give an α-amino nitrile.
A new C–C bond is formed at this step.
Step 2: Acid Hydrolysis
The nitrile group (C≡N) is hydrolyzed under acidic aqueous conditions (H₃O⁺).
This converts the nitrile to a carboxylic acid, yielding the α-amino acid.
📘 Example: Synthesis of Alanine
Aldehyde used: Acetaldehyde (CH₃CHO)
Resulting α-amino acid: Alanine (CH₃CH(NH₂)COOH)
Reaction sequence:
CH₃CHO + NH₄Cl + NaCN → CH₃CH(NH₂)CN (α-amino nitrile)
CH₃CH(NH₂)CN + H₃O⁺ → CH₃CH(NH₂)COOH (Alanine)
🧠 Important Notes:
New C–C bond is formed between the aldehyde carbon and the carbon of the cyanide ion.
This method introduces one new carbon atom into the product.
The resulting amino acid is a racemic mixture (D and L forms), unless stereoselective conditions are introduced.
This is one of the earliest synthetic routes for amino acids, including prebiotic chemistry theories.
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What two reagents are required in the first step of Strecker synthesis?
A: NH₄Cl and NaCN.
71
What intermediate is formed after reaction with NH₄Cl and NaCN?
A: An α-amino nitrile.
72
What reagent is used to hydrolyze the α-amino nitrile in Strecker synthesis?
A: Aqueous acid (H₃O⁺).
73
What new bond is formed in the first step of Strecker synthesis?
A: A new carbon–carbon bond between the aldehyde carbon and the cyanide carbon.
74
What amino acid is formed from acetaldehyde in the Strecker synthesis?
A: Alanine.
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Is the product of Strecker synthesis optically pure or racemic?
A: Racemic (contains both D- and L-enantiomers).
76
What is resolution in amino acid chemistry?
A: Resolution is the separation of a racemic mixture into its two individual enantiomers.
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Why is resolution important in biological applications?
A: Biologically active molecules like amino acids often function only in one enantiomeric form. The undesired enantiomer may be inactive or harmful.
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Why can't enantiomers be separated by common physical or chemical means?
A: Enantiomers have identical physical properties (e.g., melting point, solubility) and react identically with achiral reagents.
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How can enantiomers be separated?
A: They can be resolved by converting them into diastereomers using a single enantiomer of a chiral reagent. Diastereomers have different physical properties and can be separated.
80
Describe the three-step process for resolving enantiomers using a chiral reagent.
A:
React enantiomers A and B with chiral reagent Y to form diastereomers AY and BY.
Separate AY and BY by physical means.
Chemically remove Y to regenerate the original enantiomers A and B.
81
What is the role of the chiral reagent Y in resolution?
A: Y forms diastereomers with enantiomers A and B, enabling physical separation due to their differing properties.
82
What are diastereomers and how do they differ from enantiomers?
A: Diastereomers are stereoisomers that are not mirror images. They have different physical and chemical properties, unlike enantiomers.
83
Can resolution be avoided?
A: Yes, resolution can be avoided if enantioselective synthesis is used to prepare only the desired enantiomer from the start.
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What is the disadvantage of resolution compared to enantioselective synthesis?
A: Resolution is less efficient because half of the racemic mixture is typically wasted.
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Explanation: Resolution of Amino Acids
Goal: To separate a racemic mixture of amino acids (i.e., a 1:1 mixture of D and L or R and S enantiomers).
💡 Core Principle:
Enantiomers have identical physical properties and cannot be separated by regular means.
Diastereomers, on the other hand, have different physical properties (e.g., solubility, melting point), and can be separated by physical methods.
So, if we can convert enantiomers into diastereomers, we can then physically separate them.
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The 3-Step Strategy for Resolving Enantiomers:
Step 1: Convert enantiomers into diastereomers
React the racemic amino acids with a chiral reagent (called a resolving agent), forming diastereomeric salts or amides.
Example: Acetylate the amino acids using acetic anhydride → forms N-acetyl amino acids.
These still have one stereocenter, so they're still enantiomers.
Now react them with a chiral base, like (R)-α-methylbenzylamine.
The result: diastereomeric salts, which are no longer mirror images.
Step 2: Separate the diastereomers
Since the two salts have different melting points, solubilities, etc., they can be separated via crystallization or extraction.
Step 3: Recover the original enantiomers
Once separated, each diastereomer is hydrolyzed (e.g., using acid or base) to regenerate the original amino acid enantiomers.
🧪 Example from the Diagram:
Racemic (R)-alanine and (S)-alanine are converted to N-acetyl derivatives using acetic anhydride.
Then, these N-acetylated forms are reacted with (R)-α-methylbenzylamine.
This forms two different salts (diastereomers), which can be physically separated.
88
What is a resolving agent?
A3: A chiral compound used to convert enantiomers into separable diastereomers.
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Kinetic Resolution of Amino Acids Using Enzymes
🧠 Core Concept:
Kinetic resolution exploits the fact that enantiomers may react at different rates with a chiral reagent (in this case, an enzyme like acylase). One enantiomer reacts while the other does not, allowing them to be separated based on their differing reactivities.
🔍 Example Shown: Resolution of N-acetyl alanine
Start with a racemic mixture of:
(S)-N-acetyl alanine (from L-alanine)
(R)-N-acetyl alanine (from D-alanine)
⚙️ Step-by-Step:
Step 1: Use of Acylase Enzyme
Acylases are enzymes that hydrolyze amide bonds.
However, they only hydrolyze amides of L-amino acids.
✅ What reacts:
The (S)-N-acetyl alanine (L-isomer) undergoes enzymatic hydrolysis.
The amide bond is broken.
Result: Free L-alanine.
❌ What doesn’t react:
The (R)-N-acetyl alanine remains unchanged (no hydrolysis).
This is the D-enantiomer.
🔄 Outcome:
The mixture now contains:
Free L-alanine (with a free amine).
Unhydrolyzed D-N-acetyl alanine (with an amide).
→ These two are now physically separable because they are not enantiomers anymore — they are structurally different molecules with different physical properties.
⭐ Term: Kinetic Resolution
Separation of enantiomers based on differences in reaction rates using a chiral reagent or enzyme.
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Diastereomeric Resolution of Amino Acids
This technique separates a racemic mixture (equal amounts of (R)- and (S)-enantiomers) of amino acids using diastereomer formation via a chiral amine.
⚙️ Step-by-Step Breakdown:
🔴 Step 1: React Enantiomers with a Chiral Amine
Objective: Form diastereomers by reacting each enantiomer with a single enantiomer of a chiral amine, e.g., (R)-α-methylbenzylamine.
Start with (S)-alanine and (R)-alanine (which are enantiomers).
These are acetylated to form N-acetyl alanines, which still retain their stereocenters.
React both N-acetyl derivatives with the R-isomer of α-methylbenzylamine (resolving agent).
→ The result:
(S, R) and (R, R) diastereomers.
These now have two stereocenters and are not mirror images.
These salts have the same configuration at one stereocenter (from the chiral amine), but opposite configurations at the amino acid carbon—this makes them diastereomers.
🟡 Step 2: Separate the Diastereomers
Diastereomers have different solubility, melting points, etc., and can be separated by:
Recrystallization
Fractional distillation
Chromatography
Once separated, we now have each diastereomer isolated in pure form.
🟢 Step 3: Regenerate the Original Amino Acids
Use aqueous base (OH⁻) to hydrolyze the amide back into:
The free amino acid
The chiral amine, which can be recovered and reused.
This gives us pure (R)-alanine and pure (S)-alanine, now completely separated from each other.
🧠 Summary Concept:
A resolving agent turns enantiomers into diastereomers.
These diastereomers are physically separable.
After separation, hydrolysis restores the pure enantiomers.
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What is the 3-step resolution process?
A4:
Convert enantiomers into diastereomers using a chiral reagent.
Physically separate the diastereomers.
Reconvert each diastereomer into its original enantiomer.
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Enantioselective Synthesis of Amino Acids (Section 28.4)
🔍 Overview:
Traditional methods like kinetic resolution or conversion to diastereomers often waste half of a racemic mixture. Instead, a more efficient way is to synthesize only the desired enantiomer directly, using enantioselective synthesis.
This strategy eliminates the need to separate enantiomers and gives optically pure amino acids.
🔧 How It Works:
❗ Key Principle:
Use of a chiral catalyst to guide the addition of reagents so that only one enantiomer is formed.
⚛️ Reaction:
A prochiral alkene (usually part of an N-acetyl amino acid precursor) is hydrogenated using H₂ in the presence of a chiral metal catalyst.
The new stereocenter is created at the α-carbon (next to the carboxylic acid group).
With the right catalyst, you preferentially form either the (S) or (R) enantiomer.
🧪 Example Catalyst:
BINAP–Rhodium Catalyst
BINAP = 2,2'-bis(diphenylphosphino)-1,1'-binaphthyl.
The BINAP ligand is inherently chiral, even though it doesn’t contain any chiral carbon atoms. Its chirality arises from its 3D structure — the two naphthyl rings are oriented at right angles.
🌟 Nobel Prize:
Ryoji Noyori received the 2001 Nobel Prize for his work in developing such chiral catalysts for asymmetric hydrogenation.
🧬 Result:
With correct selection of BINAP enantiomer (R or S), you can synthesize L-amino acids like L-dopa or D-amino acids like D-phenylalanine with >99% enantiomeric excess.
