Organic Chemistry

AMINO ACID
    Amphoteric – act as acid and baseAll have chiral center (x/ glycine)L is the natural occurig form (NH2 on L)In neutral solution form zwitterion – dipolar ion at pI (isoelectric pH)
EQUIVALENT POINT
Equimolar
Mole [OH-] added = Mole [H+] present
HALF EQUIVALENT POINT
pH = pKa
TITRATION OF AMINO ACID
1. COOH deprotonated before NH3
2. 2 moles of base for 1 mole of a.a
3. Buffer capacity is greatest at pKa1 and pKa2 but smallest at pI
4. pH of equivalent point is not usually 7
5. Indicator (weak acid-not involved in rxn) – best when closest to equi. pH
HA(color 1) + H2O -> H3O + A- (color 2)
* if [H3O] > Ka, sln will be color 1
HENDERSON- HASSELBALCH EQUATION
pH = pKa – log [con. BASE]/ [con. ACID]
NEUTRALIZATION
EXOthermic rxn -> formation of something stable Always give Salt and WaterpH DOES NOT equal to 7 Depends on the acidity/basicity of the salt
BUFFER
    1. Weak Acid and salt of its conjugate base or2. Weak Base and salt of its conjugate acid 3. Use acid with pKa close to pH that you want to maintain 4. Increase [buffer] = Increase Efficiency
NON-POLAR AMINO ACID

R = CHO, Hydrophobic,↓solubilty, INSIDE or at core of proteins or transmembrane to avoid H2O
Alanine, Valine, Leucine, Isoleucine, Proline, Phenyl alanine, Glycine, Thryptophan

POLAR AMINO ACID

R= Polar, Uncharged
HydroPHILIC, ↑ solubility, on SURFACE of protein
Methioninine, Serine, Theroine, Cystein, Tyrosine, Asparagine, Glutamine

ACIDIC AMINO ACID
R = COOH group – at Physiological pH = 7.4Have 3 distinct pKa’s – 3 mole of base is needed for neutralization Important in substrate binding sites of enzymes
BASIC AMINO ACID
R= NH2 + at physiological pH = 7.43 moles of acid is needed to neutralize 1 mole of baseArginine, Lyscine, Histidine
PEPTIDE
Amino Acid subunitsPeptide bond= Amide bond formed via condensation (water is loss)Rotation about the C-N bond is limited because resonance give C-N a partial double bond character
PROTEIN
1° = sequence of a.a2° = local structure of neighboring a.a due to H-bondingα helix (keratin) β pleated sheet3°= 3D shape of protein due to hydrophilic/Hydrophobic interaction between R groups of a.a Disulfide bond → loops in protein chain Proline can’t fit into α helix → kink in chain Fibrous = sheets/long strands (collagen) Globulous = spherical (myoglobin> 4° = Arrangement of polypeptide subunit (Hemoglobin = 4 subunits)
CONJUGATED PROTEINS
Attached to prosthetic group (organic molecules or metal)
DENATURIZATION
Loss of 3D (3° structure → random coil state- disruption of INTERmolecular forces)
Due to detergent, change in pH, Temp, [solute]
Some protein can REnature
EPIMERS
Different in configuration at ONLY ONE carbon
ANOMERS
Differ in conjugation ONLY at the newly formed chiral center
KETOSE
Fructose
ALDOSE
Glucose
Galactose
Manose
MUTAROTATION
Allow α → α + β
or
β → α + β
GLYCOSIDIC REACTIONS
[image]Hemiacetal + Alcohol → Acetal Both α and β linkages are formed
DISACCHARIDES
Due to glycosidic linkages between C1-C4, C1-C6 or C1-C2
α or β
In body, enzymes ar eneeded to ensure the right glysidic bond is form.
Without enzymes, reactions are NONspecific and never stopping at disaccharide level
GLUCOSE POLYSACCHARIDES
Cellulose = β 1,4 Structure components of PLANT
Starch = α 1,4(some 1,6) Stored energy in PLANT
Glycogen= α 1,4 (some 1,6) Stored energy in ANIMAL
* Cellulose can’t be ingested by human
IR
Measure vibrations- Stretching, bending and rotation of a molecule- Stretching and bending can be Symmetric or AsymmetricLight → excited state (3500-300 cm-1
FINGER PRINT
400-1500 cm-1Characteristic of a molecule, frequently used to identify a substance
SYMMETRIC STRETCH
DO NOT show in IR because no net change in dipole moment
IR ALKANES
C-H 2800-3000
C-H 1200
IR ALKENES
=C-H 3080-3140
C=C 1645
IR ALKYNES
C ≡ C 2200
≡ C-H 3300
IR Aromatic
C-H 2900-3100
C-C 1475-1625
IR ALCOHOL
O-H (broad) 3100-3500
IR ETHER
C-O 1050-1150
IR ALDEHYDE
(0)C-H 2700-2900
C=O 1725-1750
IR ACIDS
C=O 1700-1750
O-H (broad) 2900-3300
IR KETONES
C=0(Sharp) 1700-1750
IR AMINES
N-H (Sharp) 3100-3500
C-NMR
Larger sample
NO coupling except between carbons and hydrogens directly attached to them
Spin decoupling: record without coupling of adjacent protons
Show: # of C’s with relative chemical environment
# of H’s (spin coupling NMR’s)
UV
Pass light, observe Absorbance
Beer Law
A= ebc
Most useful for studying compound wit double bonds and heteroatoms with lone pairs
MASS SPECTROSCOPY
Pass light, measure mass of particle
Sample is ruined afterward
1. cation radical decompose → mass/charge ratio
2. base peak = tallest peak (% of 100)
3. Molecular ion peak = highest m/e peak
CARBOXYLIC ACID
– suffix – ate1. Polar2. Able to form H-bond3. Greater bp than alcohol4. Acidity is due to resonance stabilization of conjugate base 5. β H’s are extremely acidic because its loss → stable carbanion6. Acidity can be enhanced by adding EN gr. or other potential resonance structre
NITRILES
aka CYANIDEhas CN- group = good [NUC-] for 1°, 2° SN2 reactions
SYNTHESIS OF CARBOXYLIC ACID
1. Oxidation of alcohol (using KMNO4)2. Ginard reagents (1 additional C)3° alkyl halide → carboxylic acid3. Hydrolysis of nitriles (1 additional C)CH3Cl → CH3CN→ CH3COOH + NH4
SOAP FORMATION
RCOOH + NaOH → ROO-Na+ (soap) + H2OSoap tends to rearrange into micelles (like mb) with polar head outward and nonpolar tails inward to dissolve greaseMicelle (as a whole) is soluable in water because of polar shell
ORDER OF REACTIVITY
Acyl halide > anhydrides> Esters> Amindes
ANHYDRIDES
= without water
2 ACID → condensation→ Anhydrides
AMIDES
[image]Form from 1° or 2° amine
HOFFMANN REARRANGEMENT
Amides → 1° with loss of carbon[image]
ESTERS
ACID + ALCOHOL → ESTER[image]
SAPONIFICATION
Fats( triacylglycerols) are hydrolyzed under basic condition
AMINES[image]
prefix amino-Boiling point is lower than alcohol because N has lower EN3° amine can’t H-bond thus have lower bp than 1° and 2°sp3 – able to undergoes nitrogen inversion (low Ea – 6 kcal/mol)* optically active if inversion is hinderedWeak Acid
DRUGS WITH AMINES GROUP
Nitroglycerine relaxants: relieve coronary arteries spasms for chest pain Nitrous oxide relaxants : dental anesthetic
GABRIEL SYNTHESIS
Primary Akyl halide → 1° amine (no side products)[image]
EXHAUSTIVE METHYLATION
aka Hoffmann Elimination [image]
MICHAEL ADDITION
[image]
ALDOL CONDENSATION
[image]
STRUCTURAL ISOMERS
Most Different
Different in MOLECULAR FOMRMULA
CHIRALITY
Chiral = nonsuperimposable
Achiral – super imposable
*rotation doesn’t change chirality
Differences in chirality can produce enantiomers (nonsuperimposed mirror images) or diastereomers ( diff, in chirality but not mirror images)
GEOMETRY ISOMERS
Different around DOUBLE BOND
cis vs. trans
Different in physicial properties (mp or bp)
Similar Reactivity
ENANTIOMERS
Chiral moleculesIdentical properties but different in optical activity
MESO COMPOUND
Chiral but not optical active because of internal plane of symmetry
OPTICAL ACTIVITY
Ability to rotate plane in polarized light
+ dextrorotary – R
– Levorotary – L
α (angle of rotation) – observed oration/ [] g/ml x leight dm
RACEMIC MIXTURE
Mixture of equal concentration of + and = enantiomers
DIASTERIOMERS
2+ chiral centers

Different in chirality but not mirror images

R,S vs. R,R

CONFORMATION ISOMERS
Different ONLY by rotation about 1 or more single bond“gauche” vs ” eclipse”
ALKANES
↑ chain length → ↑ bp, mp , density
→ ↓ bp, mp, density
Stablity of carbocation and free radical
3° > 2° > 1° > methyl
PYROLYSIS
Molecules is broken down by heat
aka: craking → radicals
NUCLEOPHILES
1. Basicity
RO-> HO->RCO2-> ROH> H2O
2. Size and Polarity
– Protic solution (able to H-bonding)
CN-> I-> RO-> HO-> Br-> Cl-> F-> H2O
– Aprotic solution
F-> Cl> Br> I
3. Larger atom = better Nuc
LEAVING GROUP
Weak acid = best
I> Br > Cl > F
SN1
Rate is dependant on the formation of carbocationCondition is chosen so that the second step is IRREVERSIBLErate = k[S]
ACCELERATE FORMATION OF CARBOCATION
1. Structural factors: more subs → more stable carbocation → better SN12. Solvent effect: Polar Solvent (better at surrounding and isolating ions) Protic polar is best (solvation stabilize intermediate)3. LG : weak bases dissociate more easily
INTERMEDIATE
Well defined species with a finite lifetime
TRANSITION STATE
Theoretical structure used to define mechanism
SN1 vs SN2
SN1
2 steps
Favored : polar PROTIC solvent
3>2>1
racemic products (loss of optical activity)
Favored the use of bulky [Nuc]

SN2
1 step – concerted
Favor: polar APROTIC solvent
1>2>3
rate = k[RX][Nuc]
Optically active / inverted products

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