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Enantiomeric excess

% of highest conc. enantiomer - % of lower conc. enantiomer

IR spectra are plotted as _____________ vs ______________

% transmittance vs wavenumber (cm^(1))

pKa of acid halide

-

pKa of +O-H

-2

∆G =

-RTln(Keq), where R = 8.314 J/mol*K Keq = [Products]/[Reactants] = [Equatorial]/[Axial]

Suffix for carboxylic acid Suffix for carboxylic acid salts Suffix for dicarboxylic acids

-oic acid -oate -dioic acids

Most hydrogen nuclei come into resonance ___ to ___ ppm downfield from TMS

0 to 10

Name the intermolecular forces from strongest to weakest

1) H-bonding (N, O, F) 2) Dipole-dipole 3) van der Waals/London dispersion

Gabriel synthesis

1) Potassium phthalimide + diethyl bromomalonate (SN2) 2) Base makes carbanion 3) SN2 w/ R-Br 4) NaOH, H2O, Δ opens ring and detaches part 5) H3O+, Δ gets rid of one CO2 and protonates the other

Good bases (5)

1) RO⁻ (oxides) 2) RC(triple bond)C⁻ (alkynides) 3) NH₂⁻ 4) H⁻ 5) ∆ OH⁻ for tertiary too!

van der Waals forces increase with...

1) Size (more important--the heavier, the stronger) 2) Shape: Ring > Straight Chains > Branched Chains (in order of decreased stacking ability)

Molecular vibrations measured by IR spectroscopy

1) Symmetric bend 2) Asymmetric bend 3) Symmetric stretch 4) Asymmetric stretch Also twisting and folding

Bulky bases (3)

1) t-BuO- 2) LDA 3) LiTMP

pKa of +N-H

10

Specific rotation is the rotation that ________ produce Opposite enantiomers produce

100% pure enantiomer (like only R or S) opposite rotation (like -10 instead of +10)

pKa of H2O

15.7

pKa of ROH

16

pKa of alpha H

20

pKa of alkyne H

25

How many stereoisomers?

2^n n = number of chiral centers

Number of hydrogens for saturated hydrocarbon

2n+2

pKa of NH3

35

1 kcal = ? J

4.184 J

pKa of alkene H

44

pKa of COOH

5

pKa of alkane H

50

A condensation reaction...

A chemical combination of two organic molecules that releases water

Universal indicator

A mixture of indicators which show different colors in solutions of different pHs ROYGBIV from very acidic to very basic

Racemic mixture

A mixture that contains equal amounts of the (+) and (-) enantiomers. Racemic mixtures are not optically active

Strecker synthesis

ALDEHYDE + NH4Cl + KCN NH4 attacks carbonyl carbon, generating an IMINE that is attacked by CN to make an aminonitrile which is hydrolyzed to make an amino acid

Organic phosphates

ATP, GTP, and those in DNA

Micelles

Absorb nonpolar organic molecules in their exterior, can be solvated w/ water due to exterior hydrophilic shell!

Aldehyde + alcohol (+ acid)

Acetal

Smallest ketone

Acetone (IUPAC name propanone)

Lewis definition of acids and bases

Acids are e- pair acceptors, bases are e- pair donors

Bronsted-Lowry definition of acids and bases

Acids are proton donors, bases are proton acceptors

Arrhenius definition of acids and bases

Acids have H, bases have OH

Nucleophilic substitution reactivity

Acyl chlorides > anhydrides > esters > amides > carboxylates

Why do carbonyl compounds have higher bp than corresponding alkane but lower bp than corresponding alcohol?

Alcohols participate in H-bonding

NMR shifts for H in: Alkyl groups Alkynes Alkenes Aromatics Aldehydes Carboxylic acids

Alkyl groups: 0-3 ppm Alkynes: 2-3 ppm Alkenes: 4.6-6 ppm Aromatics: 6-8.5 ppm Aldehydes: 9-10 ppm Carboxylic acids: 10.5-12 ppm

Ubiquinone (draw)

Also called Coenzyme Q: Biologically active quinone that is an electron carrier in Complexes I, II , and III of the electron transport chain Reduces to ubiquinol Long alkyl chain allows for molecule to be lipid soluble, carrying electrons within the phospholipid bilayer

Wavenumber

Analog of frequency used for infrared spectra instead of wavelength. f = c/λ whereas wavenumber = 1/λ

Alpha carbon

Any carbon attached directly to a carbonyl carbon

How does using base help with extracting an acid?

Base will associate with H, leaving A- behind. The A- will be more soluble in the aqueous layer b/c it's charged

Affinity chromatography

Beads are coated w/ a receptor that binds the protein of interest (high affinity), then eluted by washing the column w/ a free receptor that competes w/ the bead bound receptor and frees protein or by changing pH or salinity levels to disrupt bond b/w ligand & protein

Decalin

Bicyclic molecule

pKa trend

Bigger, more EN atoms are more acidic! (lower pKa)

Retro-aldol

Break link between ketones (acid/base cat)

Amphoteric

Can act as acid or base

Vinyl group

Carbon double bond with extra C

Highest priority functional group

Carboxylic acid

Cis alkenes have ______ heats of combustion than trans

Cis are less stable than trans, so cis have lower heats of combustion

Aliphatic

Containing only C and H (includes proline and methionine)

HCN + aldehyde (+ acid)

Cyanohydrin

IR peaks: 1900-2200 medium, 1600-1680 weak

C≡C or C≡N C=C

Peptide bond synthesis occurs with ____

DCC

Hyperconjugation

Delocalization of charge by the interaction of an empty p-orbital (often of a carbocation) with an adjacent, eclipsed sigma bond

Since the compounds in TLC are usually white, how do we see them?

Developed plate is placed under UV light or substances are stained (but this destroys them)

Types of stereoisomers

Enantiomers and diastereomers

Michael Addition

Enolate attacks an α,β-unsaturated carbonyl double bond

Aldol Condensation

Enolate ion attacks the carbonyl carbon directly Can do the E1cb after to get rid of alcohol

Which preference is best for big groups in chair cyclohexane?

Equatorial

How do we use distillation to make alcoholic drinks?

Ethanol boils at a lower temp than water; it is the condensate

3 solubility-based separation methods

Extraction, filtration, recrystallization

True/False: a single extraction with a larger volume of water us better than multiple with a smaller volume

False

Slow step in SN1/E1

First one, making the carbocation

What kind of distillation should be used if BPs are less than 25 deg apart and why?

Fractional The fractionation column increases surface area so vapor condenses on extra surfaces + refluxes back down until rising heat makes it evaporate again to do it all again higher up the column (refined sep)

Aldehyde + water (+ acid or base)

Gem-diol

Gravity filtration vs vacuum filtration

Gravity filtration is used for when the desired product is in solution (usually hot to keep product dissolved) where as vacuum filtration has the desired product being a solid

3 intermolecular forces that affect solubility

H bonds, dipole-dipole interactions, + van der Waals (London) forces

Phosphoric acid

H3PO4 Sometimes referred to as inorganic phosphate (Pi). At pH 7 exists as HPO4 (2-) and H2PO4-

Meso compounds

Have two or more chiral centers, but also have an internal line of symmetry that make them achiral. An even number of chiral centers must have opposite configurations

Hoffman/Zaitsev = thermodynamic/kinetic control?

Hoffman = lower Ea = kinetic control Zaitsev = overall lowest G = thermodynamic control

Cahn-Ingold-Prelog priority rules

How to determine priority for R/S or cis/trans

Markovnikov's Rule

Hydrogen will add to the least substituted carbon of the double bond

IR spectroscopy is best for...

ID of functional groups

n+1 rule

If a signal is split by n neighboring equivalent protons, it will be split into n+1 peaks

Amine + aldehyde

Imine + water

Strong oxidizing agents

KMnO₄ and the Cr⁶⁺ reagents

Kinetic vs thermodynamic enolate

Kinetic is with strong, sterically hindered base at LOW TEMP Thermo is with weaker, smaller bases at HIGH TEMP

Naming cyclic amides

Lactams Use B- in front to denote the letter of carbon forming bond w/ N (this tells you how big the ring is) Ex. B-lactam, gamma-lactam

Naming cyclic esters

Lactone Use B- in front to denote the letter of carbon forming bond w/ N (this tells you how big the ring is) Ex. B-propiolactone, gamma-butyrolactone

Strong reducing agent

LiAlH₄

Gas chromatography

Main difference is that eluent (usually He or N2) is an inert gas instead of a liquid. Stationary phase is a thin layer of material inside the column. Vaporize the liquid (MUST BE VOLATILE-low melting pt) before separation. Molecules are separated based on POLARITY + BP. Typically the polarity of the stationary phase matches that of the solute. Detector records material as peaks on a chart)

Saponification

Mixing long-chain carboxylic acids (fatty acids) with a strong base results in a salt called a soap plus glycerol

Ion-exchange chromatography

Molecules separated based on net surface charge by a saline

Chair flip process

Move everything over by one Axial --> equatorial Equatorial --> axial BUT up/down stays the same!

Weak reducing agent

NaBH₄

Common name of a ketone

Name alkyl groups on either side alphabetically and then add ketone Ex. 2-butanone is ethylmethylketone

Naming anhydrides

Names of parent acid(s) in alphabetical order followed by anhydride Ex. ethanoic propanoic anhydride)

Torsional strain

Neighboring carbons possess hydrogens that overlap in space

Enantiomers

Non-superimposable mirror images Opposite configuration at all chiral centers

IR peaks: 3300 broad, 3300 sharp , 1750 sharp

OH, NH, C=O

Geminal/vicinal

On the same carbon/on adjacent carbons

Why do you need to beware of reactions of organometallics with acidic hydrogens?

Organometallics act as STRONG BASES You'll RUIN the organometallic :(

Hydroxyquinone (draw)

Oxidation of quinones

Why do E2 reactions have an anti-coplanar (or diaxial) requirement?

Pi-orbitals need to overlap to create a double bond

SN2 prefers this solvent

Polar aprotic solvents because they can't H-bond and decrease nucleophilicity

SN1 prefers this solvent

Polar protic solvents because they stabilize the TS

What is the point of a boiling chip in distillation?

Provides surface area which allows for the liquid to smoothly boil

What is released in phosphodiester synthesis?

Pyrophosphate (PPi, P2O7 (4-)) Can be hydrolyzed to 2 inorganic phosphates

R vs S isomers

R: CW S: CCW

Relative vs absolute configuration

Relative: gives stereochem of compound in relation to another compound (ie D and L) Absolute: gives stereochem of compound by itself (ie R and S)

Size-exclusion chromatography

Relies on porous beads; larger molecules elute first because they are not trapped in small pores

Retardation factor

Rf = distance spot moved / distance solvent front moved

All amino acids have __ stereochem except _____

S (L), cysteine

Reagents used to transform alcohols into alkyl halides

SOCl₂ and PBr₃ (Always SN2, so only 1° and 2° alcohols)

Stereoisomers

Same connectivity, different arrangement

Diastereomers

Same connectivity, not mirror images Opposite configuration at some but not all chiral centers

Chromatography

Separates protein mixes on the basis of their affinity for a stationary phase or a mobile phase

What kind of distillation should be used if BPs are under 150 deg and are at least 25 deg apart and why?

Simple Temp isn't so high that compounds degrade

How are stereoisomers and conformational isomers different?

Stereoisomers cannot be made to be identical through rotation of single bonds

Conformational isomers

Stereoisomers that differ by rotation about one or more single bonds, usually represented using Newman projections

E2: Strong or weak Nu? TS or intermediate? Concerted or 2-step mech? Unsubstituted or highly substituted LG? Stereochemistry?

Strong TS Concerted Highly substituted Anti-coplanar (180°)

SN2: Strong or weak Nu? TS or intermediate? Concerted or 2-step mech? Unsubstituted or highly substituted LG? Stereochemistry?

Strong TS Concerted (making/breaking bond at same time) Unsubstituted Inversion

How to cleave peptide bonds

Strong acid or base

Constitutional isomers

Structural isomers: same molecular formula, different connectivity

Three polar aprotic solvents

THF, DMSO, DMF

______ is used to calibrate NMR to 0 ppm

Tetramethylsilane (TMS) SKIP THIS WHEN COUNTING PEAKS

High performance liquid chromatography (HPLC)

The P used to stand for pressure. HPLC is a type of liquid chromatography that uses high pressure to pass the solvent phase through a more finely ground stationary phase. This gives HPLC higher resolving power than regular column chromatography

Transmittance

The amount of light that passes through the sample onto the detector

Element effect for leaving group stability

The best leaving groups are more EN and bigger

Spin-spin coupling

The interaction between spin states of non-equivalent nuclei that results in a group of peaks in an NMR spectrum

Why do carboxylic acids have higher bp than corresponding alkanes and alcohols?

They are polar and H-bond well

Hammond Postulate

Transition state resembles the structure (and energy) of the reactant or product that is closest to it in energy

Naming amides

Use N to denote alkyl groups attached to nitrogen atom Ex. N, N-dimethylpropanamide

Naming esters

Use suffix -oate Substituent on one side, and then the other, counting the carbonyl carbon Ex. isopropyl propanoate

Preparative TLC

Used for purification of compound. Larger spot of sample splits into bands of individual compounds which are then scraped off + washed to reveal pure ones

Reverse phase chromatography

Uses a nonpolar card with a polar solvent

Column chromatography

Uses beads of a polar compound, like silica or alumina (stationary phase), with a nonpolar solvent (mobile phase) Different compounds migrate at different speeds

What kind of distillation should be used if BPs are over 150 deg and why?

Vacuum Vacuum lowers ambient (air) pressure, which decreases the temp the compound must reach to boil (remember liquids boil when vapor pressure equals ambient pressure)

Fischer projection

Vertical lines are into the page (dash) Horizontal lines are out of the page (wedge)

Quinone (draw)

Vitamin E and K Produced by oxidation of phenols

Reverse of extraction

Wash: add small amount of solute to dissolve impurities away from organic product

______ is removed during peptide synthesis

Water

E1: Strong or weak Nu? TS or intermediate? Concerted or 2-step mech? Unsubstituted or highly substituted LG? Stereochemistry?

Weak Intermediate 2-step Highly substituted Non-specific (no anti-coplanar)

SN1: Strong or weak Nu? TS or intermediate? Concerted or 2-step mech? Unsubstituted or highly substituted LG? Stereochemistry?

Weak Intermediate 2-step Highly substituted Racemic

When do you use a prefix for a functional group?

When it's not highest priority

Z vs E isomers

Z: cis (THINK: ciz) E: trans

Ka =

[H+][A-]/[HA]

Optical activity equation

[alpha] = alpha * c * l, where [alpha] = specific rotation alpha = observed rotation c = concentration (g/mL) l = length (dm) + = CW = d - = CCW = l

UV spectroscopy measures...

absorbance of UV light of various wavelengths passing through a sample, which causes movement of electrons between orbitals Don't need to interpret data for MCAT

UV spectra are plotted as _____________ vs ______________

absorbance vs wavelength

NMR spectroscopy measures...

alignment of nuclear spin with an applied magnetic field

Observed rotation

alpha = [alpha]*ee, where alpha = observed rotation [alpha] = specific rotation ee = enantiomeric excess

Amino acids are ______, meaning that they can act as acids or bases

amphoteric

Cyclo- and iso- are/aren't included in alphabetizing?

are

Distillation separates compounds according to differences in their ________

boiling points

Soaps contain a hydrophilic ______ head and a hydrophobic ______ tail

carboxylate, alkyl

Absorption of visible light gives ______

complementary color

UV spectroscopy is best for...

compounds w/ double bonds or heteroatoms w/ lone pairs that create conjugated systems

Is the compound with the lowest BP the condensate or the distillate?

condensate b/c it goes to the gas phase first and then condensates

Heat of combustion of alkanes ______ with branching

decreases

Diastereomers have ________ physical properties

different This includes cis/trans

Constitutional isomers have ________ physical properties

different (melting pt, boiling pt, etc.)

Protons near EN atoms produce a _______ shift

downfield THINK: deshield = downfield

Keq =

e^(-ΔG/RT), where R = 8.314 J/mol*K

Common names for methanal, ethanal, and propanal

formaldehyde, acetaldehyde, propionaldehyde

Common names for methanoic acid, ethanoic acid, and propanoic acid

formic acid, acetic acid, propionic acid

NMR spectra are plotted as _________ vs _________

frequency vs energy absorption (chemical shift δ in ppm)

With a neutral nucleophile and bad backside, ___ can favor E1 over SN1

heat

Draw the big daddy flowchart

http://lightcat-files.s3.amazonaws.com/pdfs/fgjUSGRmTna3LiOlT0K7_13A-ORGO-06j-Big%20Daddy%20Mechanism%20Flowchart.pdf

Nuclei with magnetic moments that are aligned with the field are said to be...

in the a-state (lower energy)

Bulk increases/decreases basicity?

increases

In a Fischer projection, rotating 90 deg ______ stereochem

inverts

The more a proton's electron density is pulled away, the _____ it can shield itself from the applied magnetic field

less

Superheating occurs when...

liquid is heated to above its boiling pt without vaporization--can happen when gas bubbles in a liquid can't overcome Patm and surface tension

Nuclei with odd _____, odd ______, or both will have a magnetic moment when placed in a magnetic field

mass numbers, atomic numbers

Mass spectrometry separates ions by their ________ ratio. It's then used to determine ________

mass-to-charge molecular weight

In recrystallization, the product is dissolved in a _____ amount of hot/cold? solvent and left to recrystallize as the flask cools, excluding the _______

minimum hot impurities

IR spectroscopy measures...

molecular vibrations via a change in dipole moment (bond stretching or bending) after absorbing IR radiation, looking at wavenumber (cm^(-1)) Diatomic molecules do not absorb b/c don't have dipole moment Best for ID of the functional groups present in molecules!

Molecules with a lower energy gap between HOMO and LUMO are _____ excited and can absorb _______ wavelengths (_______ frequencies) with ______ energy

more easily longer, lower lower

In the SN2 reaction, a _______ nucleophile reacts with an ________ LG to produce substitution in ______ step(s)

negatively charged accessible one

In the SN1 reaction, a _______ nucleophile reacts with an ________ LG to produce substitution in ______ step(s)

neutral inaccessible two

For E2, the number of ________ determines the number of possible products

non-equivalent B-carbons with at least one hydrogen

The more ______ a compound is, the farther it will move up the TLC gel and the ______ its Rf will be

nonpolar higher

Mobile phase is _______

nonpolar (usually the solvent that moves down the card/column)

Protic solvents hinder __________, so ____ and ____ reactions prefer them

nucleophiles, SN1 and E1

Stationary phase is _______

polar

E1 rate

rate = k[RX]

SN1 rate

rate = k[RX]

E2 rate

rate = k[RX][Nu]

SN2 rate

rate = k[RX][Nu]

Extraction is performed in a _______

separatory funnel

Stationary phase in TLC

silica gel (polar)

Filtration isolates a _______ (________) from a _______ (________) using a paper filter

solid (residue) from a liquid (filtrate)

Questions about boiling/melting points of molecules are always referring to the...

strength of IMF's between molecules

In the E2 reaction, a _______ nucleophile reacts with an ________ LG to produce beta-elimination in ______ step(s)

strong inaccessible one

The height of/area under a NMR peak is proportional to ______

the number of chemically equivalent protons

Conformational isomers have ________ physical properties

the same

Enantiomers have ________ physical properties

the same (aside from optical activity)

Symmetric stretches do not show up in IR spectra b/c...

they involve no net CHANGE in dipole moment

Extraction combines...

two immiscible liquids Nonpolar layer: organic layer (diethyl ether, on TOP) Polar layer: aqueous layer

All molecules have _______ forces

van der Waals

Strong acids are _____ bases

weak

In the E1 reaction, a _______ nucleophile reacts with an ________ LG to produce beta-elimination in ______ step(s)

weak inaccessible two

PCC is a... It can add one oxygen to ___ alcohols

weak oxidizing agent 1° (can't make beyond aldehydes)

Cis and trans for chairs is based on _________, not _________

whether substituents are facing up/down not axial/equatorial

In neutral solutions, amino acids exist as _______

zwitterions

Gibbs free energy equation

ΔG = ΔH - TΔS


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