Organic Chemistry Flashcards
1 C
meth-
2 C’s
eth-
3 C’s
prop-
4 C’s
but-
5 C’s
pent-
6 C’s
hex-
7 C’s
hept-
8 C’s
oct-
9 C’s
non-
10 C’s
dec-
-CH3
methyl
-CH2CH3
ethyl
-CH2CH2CH3
propyl
H H3C-C-CH3 I
isopropyl
-CH2CH2CH2CH3
butyl (or n-butyl)
CH3CHCH2CH3 I
sec-butyl
CH3 I -C-CH3 I CH3
tert-butyl (or t-butyl)
R2C=CR2
alkene or olefin
alkyne
R-X
alkyl halide
R-OH
alcohol
R-SH
thiol
R-O-R
ether
epoxide or oxirane
phenol
aldehyde
ketone
Hemiacetal
acetal
cyanohydrin
amine
imine
enamine
carboxylic acid
acid halide
acid anhydride
ester
lactone
amide
lactam
Nomenclature of alcohols
Hydroxyl groups noted by a suffix to the main alkyl chain
-ol replaces -e
Priorities assigned to give lowest number to hydroxyl group
Saturated
Contains on pi bonds and no rings
Unsaturated
If it has at least one pi bond or a ring
Degree of unsaturation
(2n + 2) - x/2
number of electron groups: 3
orbital geometry: ?
Trigonal planar
Number of electron groups: 4
Orbital Geometry: ?
Tetrahedral
Reactivity and Stability
Reactivity of a molecule is inverself related to its stability. Molecules that are more stable are less reactive and higher energy species will be more reactive
Inductive effects
Stabilize charges through sigma bonds
Resonance effects
Stabilize charge by delocalization through pi bonds
Resonance effect
Stabilize charge by delocalization through pi bonds
Carbocation Stabiilty trend
3 > 2 > 1 > methyl
more stable —————-> less stable
less reactive ———–> more reactive
lower energy —————-> higher energy
Carbanions Stability Trend
methyl > 1 > 2 > 3
more stable —————-> less stable
less reactive —————> more reactive
lower energy ———————–> higher energy
electron withdrawing groups
pull electrons toward themselves through sigma bonds. groups more electronegative than carbon tend to withdraw. Electron withdrawing groups tend to stabilize carbanions
Electron donating groups
Donate (push) electron density away from themselves through sigma bonds. groups less electronegative tend to donate. Tend to stabilize electron -deficient intermediates (carbocation)
Acidity strength is determined by?
The extent to which the negative charge on the conjugate base is stabilized
- Alcohols more acidic than hydrocarbons because the negative charge on the alkoxide is more stable than negative charge on carbanion
- Carboxylic acids more acidic than alcohols beause the carboxylate ion can form resonance structure leading to greater stability of the anion and to higher acidity of the conjugate acid
Acid Rank
Strong Acids > SUlfonic acids > Carboxylic Acids > Phenols > Alcohols and water > Aldehydes and ketones > sp hybridized C-H bonds > sp2 C-H > sp3 C-H
Nucleophiles
Species that have unshared pairs of electrons or pi bonds and frequently a negative charge. They are nucleus seeking or nucleus loving. Also known as Lewis bases or electron pair donors.
Nucleophilicty
-Measure of how strong a nucleophile is
Trends
- Nucleophilicity increases as negative charge increases
- Nucleophilicity increases going down a periodic table (Related to polarizability or how easy it is for the electrons surrounding an atom to be distorted. As you go down any group, atoms become more larger and more polarizable and more nucleophilic)
- Nucleophilicity increases going left in the periodic table (related to electronegativity of the nucleophilic atom. The more electronegative the better able to support its negative charge. Less electronegative, higher its nucleophilicity)
Electrophilicity
Electron deficient species; frequently have an incomplete octet; also known as Lewis acids (electron pair acceptors)
Leaving Groups
- More likely to dissociate from their substrate if they are more stable in solution
- Weak bases (I-, Br-, Cl-) are good leaving groups because their negative charge is stabilized due to their large size. Basicity decreases down a family in the periodic table that leaving group ability increases
- Strong bases are great electron donors because they cannot stabilize their negative charge very well making them very reactive . These groups are more likely to stay bound to their substrate rather than dissociate in solution. So these are bad leaving groups
Cyclopropane Ring Strain
Very strained because the carbon-carbon bond angles approach 60 degrees rather than the idealized 109 for sp3 hybridized carbond
Cyclobutane Ring Strain
Might be expected to have 90 degree bond angles but one of the C’s is bent out of the plane so that all of the bond angles are 88. The distortion minimizes the eclipsing of sigma bonds
cyclopentane and cyclohexane ring strain
Cyclopentane has low degree of ring strain and cyclohexane is strain free. Both molecules have near 109 bond angles due to conformations they adopt. These cycloalkanes do not undergo hydrogenation reactions under normal conditions and react similarly to straight chain alkanes
Constitutional Isomers
Have the same molecular formula but their atoms are connected differently
Conformational isomers
Compounds that have the same molecular formula and the same atomic connectivity but differ from one another by rotation about a sigma bond
Eclipsed and Staggered Conformations
-Anti is usually the most stable since this will minimize steric interactions
Cyclopentane Conformation
Adopts a puckered conformation because if not the C-H bonds would eclipse each other so this reduces the energy of the compound (envelope form)
Cyclohexane Conformation
If cyclohexane were planar bond angles would be 120 which would bring a lot of ring strain. Instead more stable is chair form
As one chair conformation flips to the other, it must pass through several other less stable conformations including some called (half chair) and twist boat. These are more unstable
Which hydrogen position in chair conformation more stable?
The equatorial position more stable because it is more favorable for large groups to occupy the equatorial than crowded axial position
Stereoisomers
Molecules that have the same molecular formula and connectivit but differ from one another only in the spatial arrangement of the atoms. Cannot be interconverted by rotation about a single sigma bond
dotted bond vs triangular block bond
Enantiomers
Nonsuperimposale mirror images; Always have oppsoite absolute configurations (R, S)
The chemical properties such as melting point, boiling point, polarity, and solubility are the same for both
Optical activity
- Differs between enantiomers
- Compound that rotates the plane of polarized light
- Dextrorotatory: Compound that rotates plane polarized light clockwise(+)
- Levorotatory: Compound that rotates plan polarized light in the counter clockwise rotation (-)
Magnitude = specific rotation
-Enantiomers will rotate light with equal magnitude but in opposite directions
Number of possible stereomers
2^n
Diastereomers
Molecules with multiple stereocenters
Non superimposable non mirror images
ex: R,R -> S,R
Epimers
Subclass of diastereomers that differ in their absolute configurations at a single chiral center (only one stereocenter is inverted)
When hdroxyl on right for highest number C it’s a D sugar
when hydroxyl on left, L sugar
Meso compound
internal plane of symmetry mirror image
optically inactive
Geometric isomers
Differ in orientation of substituents around a ring or a double bond
cis; high priority groups on the same side (dotted bond or block bond)
trans; high priority groups on opposite sides
Liquid liquid extraction
- Extraction allows chemist to separate one substance from a mixture of substances by adding a solvent in which the compound of interest is highly soluble
- If the solution with the compound of interest is shaken with a second solvent (completely imiscible with first) and allowed to separate in two phases the compound of interest will separate based on its solubility with each solvent
Extraction of Organic Amines
Organic compounds that are basic (amines) can be extracted from mixtures of organic compoundsupon treatment with dilute acid (5-10% HCl).
This will protonate the basic functional group forming a positively charged ion. The resulting cationic salts of these basic compounds are usually freely soluble in aqueous solution and can be removed from the organic compounds that remain dissolved in the organic phase
Extraction of Carboxylic Acids
Extraction with a dilute base (5% NaHCO3) results in converting carboxylic acids into their corresponding anionic salts
These anionic salts are generally soluble in aqueous solution and can be removed from the organic compound that remain dissolved in organic phase
Extraction of phenols
When phenols are present and need to be removed a dilute NaOH (10%) will succeed in converting phenol into corresponding anionic salt. The anionic salts of the phenols are generally soluble in the aqueous phase and can be removed from the organic phase
Extraction Example
Thin Layer Chromatography
- Compounds separated based on differing polarities
- Speed of separation and small sample amounts this method is used often
- Mobile liquid phase ascend a thin layer of absorbant (silica) that is coated onto a glass plate. This thin layer of absorbant acts as a polary stationary phase for sample to interact with
- Small amount (1 microliter) of sample is spotted near base of plate before placing plate upright in a sealed container with a shallow layer of solvent
- Solvent ascends plate via capillary action
- Separation occurs because different components travel along plate at different rates. The more polar interact more with polar stationary phase and travel at a slower rate.
- The less polar have a greater affinity for the solvent. and travel with the mobile solvent at a faster rate
- Visualization: shining ultraviolet light on plate, placing the thin layer plate in presence of iodine vapor
Rf = distance traveled by an individual component/ distance traveled by the solvent front
Column (flash) Chromatography
TLC is good for separating small amounts of material to assess how many compounds make up a mixture, but its not good for isolating bulk compounds
Chromatography column filled with silica gel and is saturated with a chosen organic solvent and the mixture to be separated is added to the top and allowed to travel down through the silica-packed column
Excess solvent added to top periodicall and flow of solvent is collected at bottom
Polar compounds spend more time adsorbed on polar solid phase and travel more slowly down column so compounds expected to leave column in order of polarity (least polar to most polar)
Ion Exchange Chromatography
-Passing mobile liquid phase with analyte through a column packed with solid stationary phase, uses a polymeric resin with + or - charged moieties on surface
The + charged groups displace sodium ions. Groups are retained (some) but the - charged pass through quickly and eluted first
-Once all neg and neutral species have been eluted the column can be treated with a concentrated sodium containing solution to displace all adsorbed positively charged species
Frequently used in separation of mixtures of proteins. IF they are passed through cation exhange resin, proteins with pI values greater than pH of mobile phase will be positively charged and elute slowly compared to those with pI values below solution pH
High performance liquid chromatography
- Takes advantage of the differing affinities for either a stationary of mobile phase
- Because mobile phase is forced through stationary phase at high pressure, speed and efficiency increase
- The sample is solubilized and injected by syringe and then the mobile phase carries sample to the column. Sample is separated into its constituent components which are detected and analyzed as they exit the column. The eluent is collected after detection and the components can be isolated after evaporation of the solvent
- Elution time is dependent on the mobile and stationary phase. Most, stationary phase is a silica gel bonded to a nonpolar group making a relatively nonpolar stationary phase (reverse phase HPLC) The mobile phase is more polar so more polar compounds will elute first as they have high affinity for mobile phase
Size Exclusion Chromatography
Technique to separate bulk materials based on molecular size
Materials to be separated are dissolved in solvent and loaded onto a column packed with stationary phase and allowed to travel to the bottom of the column where they are collected
- Stationary phase consists of porous polymer beads. Size of the pores in the beads are controlled to allow permeation of small molecules in the eluent while excluding larger ones
- Exclusion of large molecules from the pore volume creates a more direct path down the column for large species .
quick elution of large molecules and longer retention of smaller species
Affinity Chromatography
Used to purify proteins or nucleic acids from complex biochemical mixtures like cell lysates growth media, or blood rather than a reaction mixture
- Based on highly specific interactions between macromolecules
- Stationary phase is a column packed with solid resin and sample is poured through the column. -Sample is then centrifuged so the heavy solid resin settles to the bottom of the tube. Since protein of interest is bound to solid resin the liquid is simply decanted leaving the desired compound behind
- In order to isolate protein of interest, highly specific interactions of antibodies can be used specific for the protein. Protein added to isolate antigen-antibody complex. Complex is Protein of interest-antibody-protein a/g/l-solid support bead
Centrifuged
Instead of centrifuge magnetic beads can be usedto bound to protein of interest
Not all proteins of interest have an antibody available. So researchers can use an affinity tag. small molecular tag is added to N-terminus or C-terminus of protein.
Gas chromatography
Form of column chromatography in which the partitioning of components to be separated takes place between a mobile gas phase and a stationary liquid phase. This separation occurs based on differing volatilities
- Sample loaded onto syringe, injected, and vaporized by a heater in the injection port and carried along stream of inert gas.
- Vaporized sample taken into a column composed of particles that are coated with a liquid absorbant. As the ocomponents of the sample pass through the column, they interact differently with the absorbant based on their relative volatilites.
As each component exits the column it is burned and resulting ions detected by a electricla detector that generates a signal
Chart recorder enables us to determine the number of components and their relative amounts
- Less volatile comonents will spend more time dissolved in liquid stationary phase than more volatile components that will be carried along by gas at a faster rate
- More volatile emerge first
Intermolecular hydrogen bonding vs Intramolecular Hydrogen Bonding
Inter: increase the BP and MP
Intra: Decrease potential for hdrogen bond with other so BP and MP decreases
Distillation
Process of raising the temperature of a liquid until it can overcome the intermolecular forces that hold it together in the liquid phase. The vapor is then condensed back to the liquid phase and collected in another container
Simple Distillation
Performed when trace impurities need to be removed from relatively pure compound or when mixture of compounds with significantly different boiling points need to be separated.
Fractional Distillation
Used when the difference in boiling points of the components in the liquid mixture is not large. Fractional distillation column is packed with appropriate material such as glass beads or stainless steel sponge. Packing of the column results in liquid mixture being subjected to vaporization-condensation cycles as it moves up the column toward the condenser. As cycle progresses, composition of the vapor gradually becomes enriched in the lower boiling component. Near the top of column, nearly pure vapor reaches the condenser and condenses back to the liquid phase where it is collected in a receiving flask
Mass spectrometry
- Determine the mass of compounds in a sample
- Molecules ionized in a high vacuum usually by bombarding them with high energy electrons then acted on by a magnetic field This causes flight path of charged species to alter and degree to which path is changed determines the mass of the ion
Br: usually occur in two isotopes (79 and 81)
Chlorine_ two peaks 35 and 37
UV/Vis Spectroscopy
- Focuses on shorter more energetic wavlengths of radiation in UV and visible area of the spectrum
- Used to study highly conjugated organic systems
- Wavelength of maximum absorption related to extent of conjugation in the molecule (more extensive longer the wavelength)
Infrared spectroscopy
Electromagnetic radiation in the IR range (2.5-20) has the proper enegy to cause bonds in organic molecules to become vibrationally excited
When sample is irradiated, covalent bonds will begin to vibrate at distinct energy levels (wavelengths correspond to frequencies)
Double bond stretches
Carbonyls- 1700 cm
Alkenes- 1650 cm
Carbonyl peak= ver strong, very intense
Triple Bond Stretch
2260-2100 cm
O-H stretch
3600-3200 cm
Strong and very broad
C-H stretches
3300-2850
C-H 3000-2850 sp3
sp2- 3150-3000
sp 3300
Typical electrophiles for Sn2 reaction
Alkyl halides
SN2 Mechanism
The nucleophile attacks the electrophile at the same time as the leaving group leaves. The attack comes from the backside
Bimolecular; reaction rate depends on nucleophile and electrophile
Rate of reaction depends on electrophile and on degree of substitution of the electrophilic Carbon because the more bulky these groups are the harder it is for the nucleophile to gain access to the reactive site
Protic solvents hinder backside reactions so aprotic solvents used
SN1 Mechanism
