Download Amines - MCAT Cooperative

Molecular Structure and Spectra
 Mass Spec- What size and formula
 Infrared Spec- What functional groups are present
 UV Spec- Is a conjugated Pie e- system present (Single bonds alternating with multiple bonds)
 Visible Spec- 8+ double bonds (usually conjugated)
 NMR- C-H Framework
Mass Spec
 Molecules ionized by collision with high energy e- (dislodging a valence e-, and yielding a cation),
causing some of the molecules to fragment, (some +, -, and neutral). Passage of charged fragments
through magnetic field then sorts them according to their mass.
o m/z- mass:charge. z is usually one, so m/z gives mass of + charged ions.
o x-axis: mass
o y-axis: intensity
o Tallest peak (100%)- base peak, fragment in highest concentration.
o Unfragmented ion- parent peak, M+ (molecular ion)
o Variable possibilities for fragmentation- the peak furthest down the line is the unfragmented
cation. For distinguishing between fragments and possible starting molecules, look at
possible structures and what may easily be lost as a fragment.



Alcohols- 2 pathways of fragmentation
1) alpha cleavage- C-C bond nearest OH is broken neutral radical plus charged O containing
fragment.
2) Dehydration- H2O eliminated yielding a alkene radical with a mass 18 units less than M+
Amines- Aliphatic amines undergo similar alpha cleavage as for alcohols. C-C bond nearest N is broken,
yielding an alkyl radical and a N containing cation
Carbonyl Compounds- ketones and aldehydes with an H on a C 3 C’s away from carbonyl C (not
counting carbonyl C) undergo McLafferry Rearrangement: H is transferred to carbonyl O, C-C is
broken, neutral alkene is formed and charge remains on O containing fragment.
o May also undergo alpha cleavage, C next to carbonyl is cleaved off and charged stays with O
containing compound.
Absorption Spectroscopy
 Infrared- detects what functional groups are present
 Visible- detects 8+ double-bonds, usually conjugated
 Ultraviolet- detects conjugated double-bonds: C-C=C-C=C-C
IR: IR spectrum  what molecular motions  what functional groups
 Wavelengths in um
 Frequencies in wavenumber (reciprocal of wavelength in cm)
 Useful from 4000 to 400cm-1
 How it works:
o All molecules have a certain amount of energy distributed throughout structure, causing bonds to
stretch and contract, atoms to wag back and forth, and other molecular vibrations to occur.
o A molecule can stretch or bend only at specific frequencies corresponding to specific energy
levels.
o When a molecule is irradiated with electromagnetic radiation, energy is absorbed if the
frequency of the radiation matches the frequency of the vibration.
 Divide IR (4000 to 4000 into 4 regions)
o 4000-2500: N-H, C-H, O-H
o 2500-2000: Triple bonds (CtbC, CtbN)
o 2000-1500: Double bonds (C=O, C=C, C=N)
o 1500-400: Fingerprint region (most complex region of IR)
*Short strong bonds vibrate at a higher frequency and energy than long weak bonds. Small
weights>TB>DB>SB.
Visible region
 8+ double bonds, usually conjugated
 e.g. Beta carotene 11 c=c max absorbance at 497, looks orange
UV: bombard with UV over changing wavelength, 200-400 nm
 detects conjugated C=C (isolated C=C don’t change spectrum)
 change in E of molecular orbitals, increase 30-40 nm for each additional C=C, increase 5 nm for each
additional alkyl group
NMR
 Map of Carbon-Hydrogen framework (Can tell the protons and their environment)
 Sample in magnetic field, nuclei align with field. Bombard with electromagnetic energy, and at the
resonance frequency, the nuclei turn to face against the magnetic field. Peak above 10=acid=free proton.
Distinguish and count atoms in different locations in the molecule.
 Electron environment of proton (shielding). Electrons shield surrounding protons from the magnetic
field. More shielded= right shift. Shifted left by adjacent groups that are electron withdrawing.
 Integral is the number of equivalent protons (CH3 integral value of 3), area under the peak.
 Spin-Spin splitting: split into n+1 where n= the number of adjacent different hydrogens (CH3-CH3 all
equal so no splitting) (CH3 – CH2Br triplet, quartet)
http://www.cem.msu.edu/~reusch/VirtualText/Spectrpy/nmr/nmr1.htm#nmr1
Type of proton.
Chemical shift ( ppm)
Alkyl, RCH3
0.8-1.0
Alkyl, RCH2CH3
1.2-1.4
Alkyl, R3CH
1.4-1.7
Allylic, R2C=CRCH3
1.6-1.9
Benzylic, ArCH3
2.2-2.5
Alkyl chloride, RCH2Cl
3.6-3.8
Alkyl bromide, RCH2Br
3.4-3.6
Alkyl iodide , RCH2I
3.1-3.3
Ether, ROCH2R
3.3-3.9
Alcohol, HOCH2R
3.3-4.0
Ketone, RCOCH3
2.1-2.6
Aldehyde, RCOH
9.5-9.6
Vinylic, R2C=CH2
4.6-5.0
Vinylic, R2C=CRH
5.2-5.7
Aromatic, ArH
6.0-9.5
Acetylenic, RC=CH
2.5-3.1
Alcohol hydroxyl, ROH
0.5-6.0a
Carboxylic, RCOOH
10-13a
Phenolic, ArOH
4.5-7.7a
Amino, R-NH2
1.0-5.0a
Separations and Purifications
Extraction- transferring a solute from one solvent to another.
 Solute more soluble in second solvent than in first.
 Solvents:
o must not be miscible (mix freely)- like dissolves like
o must form two separate layers/phases
Distillation- vaporizes a liquid, condense the vapor, collect condensate into another container.
 Separate mixtures with different boiling points
 Simple distillation- separates only by differences in boiling point and will not separate a mixture into
pure components.
 Fractional distillation- initial sample of distillate is continuously redistilled, thus at each point the
sample boils at a lower and lower temperature, ultimately approaching the boiling point of the pure
substance with the lower boiling point.
o Accomplished by the use of fractional distillation column, packed with a suitable material which
subjects a mixture to repeating vaporization-condensation cycles until a pure substance emerges.
Chromatography- separation of a mixture of two or more different compounds or ions by distributing them
between two phases: one stationary, and one moving.

Column chromatography (solid-liquid)-
o Solid phase- typically aluminum or silica gel, (more polar functional groups will form stronger
bonds).
o Column packed with solid (stationary phase), and the liquid (moving phase) is poured through
the column. Dynamic and constantly changing equilibria. Solutes will initially bind to aluminum
at the top, but will be rinsed to the bottom, creating bands of different solute concentrations.

Thin-layer chromatography (solid-liquid)o Thin layer plate or slide is the solid phase, (typically polar)
o Plate is spotted with mixture of interest.
o The plate is placed in a developing chamber some volume of solution on the bottom. The spots
must lie above the surface of the solution in the chamber. The solution will rise up the plate by
capillary action (moving phase, usually less polar than solid phase).
o Components in the mixture will separate according to their polarity.
 Polar substances will move slowly or not at all due to their affinity for the stationary
phase.
 Non polar substances will move more rapidly and further due to their affinity for the
mobile phase.

Paper chromatography (liquid-liquid)o Sample is spotted onto filter paper
o Paper is placed into developing chamber
o Water is the stationary phase (cellulose absorption)
o As developing solvent moves up the paper (through capillary action) the components of the
mixture separate due to water solubility, those most soluble and greatest propensity for hydrogen
bonding are held back.

Gas chromatography (gas-liquid)o Separates components of a mixture primarily on the bases of their vapor pressures (or boiling
points)
o Column is packed with a liquid (stationary phase)
o Carrier gas is allowed to flow through the column supporting the liquid phase.
o Mixture of compounds to be separated is introduced to the carrier stream.
o Length of time required for a sample to move through the column is a function of how much
time the sample spends in the vapor phase and how much time it spends in the liquid phase. The
more time the sample spends in the vapor phase, the faster it gets to the end of the column.
o More volatile component arrives at the end of the column first.
Biological Molecules
Carbohydrates
 Classification
o Simple- monosaccharides
 Aldoses and Ketoses
o Complex- two or more simple sugars linked together by glycosidic linkage.
 May be alpha or beta depending on the position of the hydroxyl group on carbon #1.

Anomers: isomeric forms of monosaccharides that differ only in their configuration about
the anomeric carbon, (carbonyl carbon prior to hemiacetalation or hemiaketalation.

All carbohydrates are chiral
o Fischer projections are used to show absolute configuration around chiral center
 Horizontal lines- project out of the page
 Vertical lines- project into the page
 The last chiral center in an aldose chain (farthest from the aldehyde group) was chosen by
Fischer as the D / L designator site
 D: if the hydroxyl group in the projection
formula points right
 L: left directed hydroxyl group (the mirror
image) then represented the L-family.
 Absolute configuration, which is different
from d/l (dextra/levarotary +/-) relative
configuration based on rotation of light.
 D sugars are the natural form we can digest.
 Note L and D different from l & d which correspond to rotation of plane polarized
light.

Cyclic structure and conformations of hexoses
o Many simple sugars can exist in a chain form or a ring form (intramolecular hemiacetals or
hemiketals)
o The ring form is favored in aqueous solutions
o The glucose ring: oxygen on carbon 5 links with the carbon 1 and transfers its hydrogen to the
carbonyl oxygen to create a hydroxyl group.
o alpha glucose when the hydroxyl group is on the opposite side of
the -CH2OH group (away)
o beta glucose when the hydroxyl group is on the same side as the CH2OH group (by).
o Isomers, such as these, which differ only in their configuration
about their carbonyl carbon atom are called
anomers. The carbon about which this rotation
occurs is the anomeric carbon.
o Structures that have opposite configurations of a
hydroxyl group at only one position, such as
glucose and mannose, are called epimers.

Hydrolysis of glycosidic bond
o Hydrolysis of starch involves the cleavage of the
acetal functional groups with the addition of a
molecule of water for each glycoside linkage
o Hydroxyl group reacts with anomeric carbon
o Produces many molecules of glucose
o This is done by the enzymes called glycosidases or amylases which are found in saliva.
o These enzymes work only on alpha glycoside linkages and do not attack beta linkages. Such
beta linkages are found in cellulose.
o Glycogen has alpha 1-6 (branching) and1-4 linkages
Amino Acids and Proteins
 Description
o Basic structural unit of proteins
o Absolute configuration at alpha position
 All are α-amino acids with carboxyl group, amino group, hydrogen and variable R group
attached to a central α-carbon
 R groups vary in structure, size and charge and influence solubility of the amino acid
o Amino acids as dipolar ions classification
 Each amino acid has an isoelectric point at which the amino acid exist as the neutral,
dipolar zwitterions seen above.
o Classification
 Acidic or basic- amino acids are amphoteric; they can react as acids or bases depending
on the circumstances.

Hydrophobic or hydrophilic
 Reactions
Peptide linkage- covalent bond that joins amino acids together. Amide bond is formed between two adjacent
amino acids; commonly called the peptide bond or peptide linkage.
 Formed by a condensation reaction involving the loss of water
 It is formed between the alpha-amino group of one amino acid and the alpha-carboxyl group of another
amino acid
 The peptide bond is rigid due to resonance and partial C=N
character. The six atoms in the peptide bond are in a flat
plane.
 Serine becomes seryl, glycine becomes glycyl, alanine
becomes alanyl etc.
Hydrolysis and Dehydration Synthesis
 Hydrolysis: the reverse reaction
 Peptides and proteins chains have direction because the
chains have different ends, an alpha-amino end and an alphacarboxyl end
 By convention the amino end is taken as the beginning of a chain
 An amino acid sequence is written starting from the N-terminal amino end
 Thus the tripeptide gly-ala-leu is not the same as leu-ala-gly because the former has gly at the Nterminal and leu at the C-terminal whereas the latter has leu at the N-terminal and gly at the C-terminal.
Chemically, in the former gly has a free amino group, and in the latter leu has a free amino group.

General Principles
o Primary (1º) structure: sequence of aa residues
o Secondary (2º) structure: αβ structural patterns formed by interactions between peptide planes
o Tertiary (3º) structure: 3-D folding/shape
o Quaternary (4º) structure: arrangement of 2+ subunits, if present, to form a multimeric protein
Lipids
 Description; structure
o Lipids have hydrophobic (long hydrocarbon tails) and
hydrophilic (charged heads) ends
o Lipid bi-layers (phospholipids) make up cell membranes
o Molecules with polar and non-polar groups are called
amphipathic

Steroids Steroids have a four ring structure
 Cholesterol, a steroid derivative, is essential to fluid nature of the cell membrane
 Cholesterol decreases the melting point and increases the boiling point.
 Bacteria do not make steroids.

Terpenes




Widespread in nature, mainly in plants as constituents of essential oils.
The building block is the hydrocarbon isoprene
Terpene hydrocarbons have molecular formulas (C5H8)n
Triacylglycerols
 Glycerol backbone with three carboxylic acid derivatives








Saturated: no double bonds; i.e. saturated with hydrogen
Unsaturated: has double bonds. Double bonds can be cis or trans and are bent. The
more unsaturated means more irregular structure and a lower MP
Shorter chains also have a lower MP (fewer vDW interactions)
Lipases and phospholipases are enzymes that break up lipids
Treatment with NaOH (saponification) breaks the fat into glycerol and fatty acids. Soap
used to be made this way
The Ca2+ ion in water, known as hard water, cross links the head groups causing the soap
scum
Natural glyceraldehydes are always D
Free fatty acids
Phosphorous compounds
ATP, ADP, TTP, GTP, CTP, UTP, Insecticides, phosphatidyl choline, protein phosphorylation, cell signaling
There is a large amount of energy stored in phosphoric acid bonds, so it is used for energy storage
P-O-P is the phosphoric anhydride bond (high energy). C-O-P is the phosphoester bond.