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153 Cards in this Set
- Front
- Back
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Formula for Specific Rotation
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alpha = (observed rotation)/(tube length in cm)(conc. in g/mL).
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Aliphatic
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Hydrocarbon without any aromatic rings
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BHT (GS)
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Butylated Hydroxytoulene. A resonance stabilized radical used in packaging to terminate harmful free radicals.
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ESR (GS)
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Electron shell repulsion. Explains why substituents are in equatorial vs axial positions (large ones especially).
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Paraffins
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What alkanes used to be called since they did not react.
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Markovnikov Rule
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The special group attaches to the most substituted carbon and the hydrogen attaches to the least
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Anti-Markovnikov (when?)
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When the reaction involves radicals. It also occurs with bromine and peroxides (but not with other halogens).
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Huckel's Rule
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4n+2 pi electrons. Recall that each pi bond as two pi electrons! This is a characteristic of cyclic compounds being aromatic.
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What are the special numbers determining if a hydrocarbon is gas, liquid, solid?
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1-4: gas
5-17: liquid >17: solid |
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What happens to MP and BP when MW increases?
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Both increase.
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What happens to MP and BP when Branching increases?
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MP increases. BP decreases.
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Melting point vs Boiling point
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melting point is dependent on the packaging. BP is dependent on the intermolecular forces.
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Carbon prefix for 11C
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undec-
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Carbon prefix for 12C
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dodec
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Sigma Bond
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electron density shared between the nuclei of the two atoms
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Pi Bond
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no electron density shared between the nuclei but rather only above and below the internuclear region.
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Q: Why does Flourine have a lower bond dissocation energy than Chlorine?
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It is the only diatomic molecule with no sigma, but only one pi. Accounts for its small size as well.
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Sigma Bond First Rule
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This rule states that sigma bonds form first, then the pi bonds. Flourine is an exception.
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HONC-1234
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Hydrogen = 1 bond
Oxygen = 2 Bonds Nitrogen = 3 Bonds Carbon = 4 Bonds If they become each other, you have a charge, alt to valence table |
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Homolytic Cleavage
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Breaking of a chemical bond into two free radical fragments.
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How do you calculate the strength of force in an ionic bond?
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Coulomb's Law:
(1/4pi.epsilon)(q1q2/r2) epsilon = 8.85 x 10^-12 |
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What are the five main "excuses" that dictate electron density, stability, and thus reactivity?
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1. Resonance
2. Inductive Effect 3. Steric Interactions 4. Aromaticity 5. Hybridization |
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Fonclbrisch
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The order of electronegativity - important in determining inductive effects.
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Which is a better nucleophile: (ch3)3N or (ch3)2NH?
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(CH3)2NH. Though it has less electron donating groups, the other answer has more steric hindrance. (tipping point is here)
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Huckel's Rule
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2n + 2 pi electrons where n=0,1,2,3,4,5,6, etc.
A double bond equals 2 e-. |
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How can we determine the acidity of a compound?
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By looking at the stability of the conjugate base.
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What is the key difference between Bronsted-Lowry acid and Lewis Acids?
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Lewis acids dont always need a protic hydrogen to accept electrons. It can just be an empty valence shell.
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Classic lewis acids.
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ex. BF3, AlCl3, FeBr3, SOCl2
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Classic Bronsted Lowry Acids.
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H2SO4. HNO3. HCl. HBr.
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Nucleophile
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A molecules that seek out the nucleus or positively charged sites
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Electrophile
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Molecules that seek out negative charged sites or ones that get attacked.
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- How can the hybridization tell you about the strength of the acid or base?
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The more s character means stronger acid, the more p character means stronger base.
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What attraction actually exists between non-polar tails in a micelle?
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BI I PaVII P49.
Vanderwaal's forces. hmm |
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Describe the relationship between acid/base and its conjugate base/acid in terms of their pka/b.
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pka + pkb = 14. !.
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What is the general formula for alkanes?
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CnH2n+2
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What is the general formula for alkenes? What other group has this same formula?
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CnH2n
Cyclic alkanes |
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What is the general formula for alkynes?
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CnH2n-2
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If two groups switch once on a stereocentre then...
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ENANTIOMERS
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If groups switch TWICE on a stereocentre, then...
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SAME
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TWO Stereocentres: if two groups switch one both, then
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ENANTIOMERS
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TWO stereocentres: if two groups switch only one 1/2, then
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DIASTEREOMERS
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Which (3) physical properties do diastereomers differ?
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- MP
- BP - density |
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Envelope Shape
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The shape of cyclic pentanes where 1 carbon is not coplanar with the rest!
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How do we calculate the total number of stereoisomers based on the number os stereocenters?
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2^n of stereoisomers where n = number of stereocentres.
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Anomer
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Any diastereoisomer of a sugar or derivative differing in configuration only at C-1 of an aldose or C-2 of a ketose
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What does it mean to not be optically active compound?
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- This does not refer to a racemic mixture since it consists of optically active compounds.
- it refers to meso or achiral compounds only! |
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What is enantiomeric excess and how do you calculate it?
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EE occurs when racemic is not 50:50. It is the DIFFERENCE in percentage of the more abundant and less abundant.
ee = (measured specific rotation)/(specific rotation of pure enantiomer) x 100%. NOTE HOWEVER, that this is the DIFFERENCE and not the actual value (BI IV p. 203) |
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**When ever does the hydride shift occur?
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When a carbocation is right near to a carbon capable of TERTIARY potential.
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Chiral Auxillaries
eg? |
A group of enzymes that specifically react with certain S or R isomers: they can introduce another chiral centre and create a diastereomer, or introduce a FG into the existing chiral centre which ALL would change the physical characteristics.
eg. porcine renal acylase |
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When the question is asking which results in more asymmetric carbons, what does that mean?
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BI III Pa13.
- Asymmetric Carbons refers to stereocentres. Makes sense now,. |
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What is the order to reactivity of the carbonyl group?
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Acid halide> Anhydride> Ester > Acid > Amide
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Tautomerization
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Structural isomers that vary in the position of the pi bond and a hydrogen! Between ketones and enols.
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How do you judge whether a leaving group is good?
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First, you assume when that LG leaves, it binds to a hydrogen to return to neutral. Then look at the pKa of that compound.
THE LOWER THE BETTER LEAVING GROUP! |
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What kind of X should an alkyl halide be attached to if we wanted to grow a compounds C number?
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IODINE! especially during the deprotonation of ALPHA protons in carbonyl groups.
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What is a Lactone? How do you make lactones?
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A cyclic ester!
- Needs a hydroxy ester (where the hydroxy group is on gamma or delta) - Baeyer-Villeger reaction |
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Baeyer Villiger Reaction
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Cyclic Ketones + Peroxyacids (RCO3h) = Lactones
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Transesterfication.
What does the entropy tell you about this reaction? |
When an alcohol is added to an ester, it can substitute the OR group with the alcohol.
- There is nochange in entropy and enthalpy is of no sig, therefore the equil constant is 1! This reaction is therefore reliant on LeChatlier's Principle. |
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Aldehyde + xs Alcohol under ACIDIC conditions?
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Acetal
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Aldehyde + xs Alcohol under BASIC conditions?
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Hemiacetal
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Ketone + xs Alcohol under ACIDIC conditions?
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Ketal
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Ketone + xs Alcohol under BASIC conditions
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Hemiketal
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How can we protect carbonyl groups? How is this protecting group removed?
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a DIOL (usually a 1,2 diol) under acidic conditions.
- it is removed by adding water. |
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Tetrahedral Intermediate
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an intermediate most common for substitution reactions in carbonyl groups. The double bond O always breaks in this intermediate.
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What are the some ways to differentiate between Ketones and Aldehydes (no oxidizing tests and such yet) (4)
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- HNMR
- CNMR - UV absorption (differing pi bonds) - Reactivity |
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Kinetic Enolate
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- With bulky bases or under cold temperatures, the enolate will form with the least substituted C.
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Thermodynamic Enolate
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With small bases or under high temp, the enolate will form with the more substituted C.
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How does the boiling point compare with alkanes and ketones/aldehydes?
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Not much of a difference since there are no hydrogen bonds involved!
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What stops the oxidation of an alcohol to an aldehyde? Describe what this stands for and what chemical compounds are actually involved.
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PCC.
Pyridinium Chlorochromate CrO4, HCl and pyridine. |
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LiAlH4 vs NaBH4.
What are the secondary conditions? |
LiAlH4 reduces everything
NaBH4 reduces only ketones and aldehydes 2. Add NH4Cl |
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How can we make aldehydes/ketones back into alkanes?
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1. Clemmensen reduction
2. Raney nickel reduction 3. Wolff-Kishner Reduction |
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Clemmensen reduction
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Zn(Hg)/HCl
-reduces ald/ket to alkane, but not strong enough for acids-esters. |
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Raney Nickel
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Dithiol and Raney Nickel (fine nickel with Al2O3).
- reduces ald/ket to alkanes |
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Wolff-Kishner.
KNOW THIS MECHANISM |
Uses hydrazine and water/base to reduce ald/ket to alkane
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How do we protect alcohol? Deprotect?
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- Add (CH3)3SiCl to convert alcohol into an ether
- Deprotect with NaF or acid. |
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How can we make a malonic ester undergo cyclization?
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Addition of hydrazine p.44.
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What sort of reaction can we do with the product of Claisen condensation: acetoacetic ester? (2)
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1. With a primary halide, increase the number of C on the alpha C.
2. in acidic water and heat - hydrolyze the ester into a B-ketoacid then decarboxylate |
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How do the products of an unsymm ketone differ under cold and hot for aldol reaction?
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Kinetic Aldol
Thermo Aldol |
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What is the usual product for an aldol reaction?
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a,B unsaturated compound. It readily undergoes dehydration
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What is the difference between aldol and claisen? What is the product of claisen?
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Aldol uses ketones while claisen uses esters.
- the product of claisen is the b-ketoester. |
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Saponification
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base catalyzed hydrolysis of fats and glycerides.
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Wittig Reaction.
What is the key step in making the ylide reactive? After reacting with a ketone, what is the usual product? |
- P(C6H5)3 with a primary halide to make a P - C compound.l But you need Li-but to make the C negative.
- the ylide will react with the double bond 0 to make an alkene with the C attached. It is in an E fashion!! |
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Pinacol Rearrangement.
Starting: a highly substituted diol and acid. |
p. 40. NEW. With a diol under H2SO4, we have a ketone forming an a methyl shift. Draw out the mechanism.
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Where do catabolic and anabolic reactions usually occur in the body? Which is reductive and oxidative.
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CATABOLISM - OXIDATIVE - occurs in the mito matrix
ANABOLISM - REDUCTIVE - cytoplasm. (glycol is exception) |
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Why is FADH2 doubly reductive?
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One H acts as a hydride while the other is gained as a proton.
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What is the Tollen's reagent?
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Ag(NH3)2+ that only reacts with aldehydes and alpha hydroxy ketones. A chemical test for differentiation.
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Decarboxylation
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Only for B-Ketoacids where the addition of heat releases CO2 from the compound.
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Diekmann Condensation
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Like Claisen, but with a diester far apart enough for five or six membered ring formation.
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Simple Distillation vs Fractional Distillation
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Both can have a distillation column, but in simple, this column would empty, while in fractional this would be filled with material to increase the SA. With this fractional material, the number of evap/condens cycles increases, which purifies the final product.
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When do we want to use vacuum distillation?
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Vacuum distillation will lower the BP of the reactants, where we would want to use this for reactants that have high BP, higher than the flash point or decomposition point
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Adsorbent.
Two examples? Polarity? Which one is more polar? |
In chromatogaphy, this is the stationary phase. Two common ex are alumina or silica gel. Both are polar, but anhydrous alumina is more polar than anhydrous silica gel.
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Why do we use that extra sheet of paper during TLC?
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It soaks up the solvent higher, which allows for more evaporation to occur, saturating the jar air with the solvent!
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What are the (3) ways to DEVELOP a TLC plate?
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1. spraying ninhydrin
2. iodine crystals 3. UV light |
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How do you determine the Rf value in chromatography? What is a good Rf value?
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Rf value = distance (solute)/distance of solvent
Good Rf values are the ones with the greatest multiplicative difference (not additive). ex. 0.1 and 0.2 (diff is x2) vs 0.2 and 0.3 (x3/2). Hence the first is better! |
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What is the purpose of the sand in chroma columns?
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This ensures that the surface is flat, so that components all travel the same exact distance through the silica gel.
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Elution Time
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The time it takes to travel the length of the chroma column and drip out
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Antigen Column
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More in biochemistry, it binds to certain antibodies in the solution, To reverse this binding, add salts to increase the ion conc or add more free antigen to disengage.
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Chiral Column
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Chiral compounds associate with one another. Therefore, if you wanted to isolate S, you would want to use a R column, which would increase the elution time compared to the R enatiomer,
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What are the 3 diff common designer polymers
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1. sulfonated-polystyrene
2. CM cellulose 3. DEAE-cellulose See other FE for which amino acid they bind. |
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Sulfonated Polystyrene.
Which aa does it specialize in binding? |
Negatively charged. But because it is usually done at a low pH, it binds everything, but the pH can be slowly increased to release certain aa/protein.
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Carboxymethyl-cellulose (CM Cellulose)
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Negatively charged. Done at neutral pH. Therefore, binds to proteins with high pI values (or the basic aa)
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Diethylaminoethoxy-cellulose (DEAE-cellulose)
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Postively charged at neutral pH. Therefore, binds to proteins with low pI (or the acidic aa)
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What are some characteristics of the reactant in order to undergo Gas Chromatography?
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Highly volatile at 200C and inert to silica gel or wax for GC analysis.
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Gas Chromatography characterisitics.
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It uses inert gases like helium or argon. The ones with the lowest elution times reach the detector first, peaking first. Therefore, the graph is read right to left! Purity is relative to the number of peaks, while abundance is the height. Mass of the molecule along with the polarity of it (column is polar) determines the elution time.
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Brine Solution
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A highly concentrated salt solution to increase the difference between two layers in extraction.
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how would we be able to separate a weak acid from a strong acid in extraction.
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RULE OF THUMB: add the weak base before the strong base. The weak base will selectively react with the strong acid before the weak acid.
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What reactants can't we use extraction for?
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Water sensitive componds like acid anhydrides, acid halides, or esters.
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How do we effectively remove coloured impurities from a mixture?
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add charcoal!
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During recrystallization, what kkind of solvent do we want to use for washing?
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A solvent that does not dissolve the reactant, but can wash away the recrystallization solvent (non-polar could still wash away polar). and highly volatile so it can evaporate.
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How does the BP change in a racemic mixture to one with a pure enantiomer?
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The enantiomers in a racemix mixture interact with one another moreso than in a pure solution. Therefore, the BP decreases in relativity when in a pure enantiomer solution.
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how can we determine the density quickly without them giving it to you?
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DUH, the molecular mass.
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bromine water - chemical test
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reacts with alkenes to change from a brown to clear solution
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iodoform test - chemical test
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reacts with methyl ketones to change from a clear solution to the appearance of a yellow precipitate.
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IBr chemical test
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reacts with unsaturated fats to change from purple to clear
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K2CrO4 chemical test
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reacts with 1 and 2 alcohol and aldehydes to change from orange to green!
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Chlorine isotopes and the ratio of peaks in mass spectroscopy.
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Cl-35 and Cl-37 with 35 being more abundant. In a mass spectroscopy, we would see a 3:1 peak height, with a 2 amu difference. (PARENT PEAK)
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Bromine isotopes and the ratio of peaks in mass spectroscopy
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Br - 79 and Br-81, with both in equal amounts. In mass spectroscopy, expect to see a 1:1 ratio with a 2amu difference (PARENT PEAK)
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Parent Peak vs base peaks in mass spectroscopy
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Parent: peak of the highest mass (relatively higher in that region)
Base peak: the peak with the highest abundance. In mass spectroscopy, usually a methyl, ethyl, or a heteroatom is cleaved off! |
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Why do we want to conduct mass spectroscopy under low pressure and in gas?
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we want the particles to move independently - therefore gas phase. Low pressure - since radicals are beings formed, in a high pressure, these radicals would combine to create new compounds.
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His Lies Are Basic
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Basic Amino Acids:
- histidine, lysine, arginine |
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The Acidic Amino Acids
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Glutamic Acid
Aspartic Acid |
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Leusing Valor from all their phobia is so a guy's thing.
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Hydrophobic Amino Acids:
- leucine, valine, alanine, isoleucine, glycine |
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Phree or eighty semi-pros tripped into me thigh.
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Semihydrophobic
- phenylalanine, proline, methionine, tryptophan. |
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Glue sero to three cysts onto asparagus in water then tie rope.
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Hydrophillic Amino Acids:
-glutamine, serine, threonine, cysteine, asparagine, tyrosine. |
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What are the two aa that contain a thiol group?
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Methionine and cysteine
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What are the 8-10 essential amino acids (depending on your age)?
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The fact that eighty three LIons tripped into me thigh is so leusing valor! Charge a fee and (tie his rope!)
- (8) phenylalanine, threonine, lysine, tryptophan, methionine, isoleucine, leucine, valine. - sometimes tyrosine and histidine. |
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what is special about the structure of histidine - why doesn't it have a positive charge at pH of 8 like the other basic amino acids?
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The side chain is in the form of a ring structure with the 2N in the imidizole ring and hence has no positive charge even at pH of 7. SEE II p.180
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What are some structural features that cysteine and proline provide for a protein?
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-cysteine is responsible for those disulfide cross-bridges - which increase the packing (liquid to solid)
- proline is cyclic, and therefore causes turns in the protein. (II p. 181) |
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what is the difference in calculating the isoelectric point for acidic/neutral amino acids, v basic amino acids?
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REMEMBER the whole purpose of the isoelectric point is to find the pH where the zwitterion exists (neutral molecule) play around.
- acidic/neutral: (pka1 + pka2)/2 - basic: (pka2 + pka3)/2 |
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How do we determine the isoelectric point of a protein (dif from just amino acids!) But the question is, how do we determine the value of the pKas to use.
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Summing the number of basic amino acids and the N terminal (assuming the pH is at 1), and taking the pKa of that number and the subsequent pKa and dividing it by 2. 6
let's say it was pka3 and pka4. How do we determine these values. LOOKING at the protein, the order of pka is in NUMBERICAL ORDER with Pka1 also starting with the carboxyl terminal |
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What are the 3 major chemical reasons for the secondary structure of the protein
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1. Hydrogen Bonding
2. Disulfide Bridges 3. Kinks and turns from prolines |
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How does the hydrogen bonding differ between a-helices and b-pleated sheets?
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in a-helices, the hydrogen bonding is between two neighbouring residues. (3.4aa per turn and each turn is 5.4A in length)
in B pleated sheets, the hydrogen bonding occurs between the nitrogen and the carbonyl oxygen. |
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How can we break a disulfide bridge and why is this possible? (side ques: what drives cross-linking - enthalpy or entropy)
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First of all, a disulfide bridge is created when two cysteines lose an H, and bind to each other. The loss of H indicates an oxidative process (one of the few that is anabolic). Anyways, to break one is to add a reducing agent like B-mercaptoethanol (HSCH2Ch2OH). Enthalpy drives the reaction and not entropy - think about it.
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isoelectric focusing (gel electrophoresis)
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This technique utilizes the different isoelectric points of proteins and sets a pH gradient. once the protein finds their isoelectric pH, they become neutral where they are no longer influenced by the (-) charge. (see the other gel electrophoresis for proteins)
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SDS Gel Electrophoresis
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SDS (sodium dodecyl sulfate) adds SDS into the protein structure where every residue takes on a (-) charge. This results in every protein having an equal mass:charge ratio, where these proteins are separated from their mass alone.
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Sanger's Reagent
- what is the use? - what is the structure |
2,4 dinitrofluorobenzene (see p.II 196 for structure). It specifically binds to the first amino acid!
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What are the cut sites for the following three enzymes: chymotrypsin, trypsin, and pepsin.
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Chymo: C side of Phe, Trp, Tyr
Trypsin: C side of Lys and Arg (2 basics) Pepsin; C side of Asp, Glu, and Leu |
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Edman's Reagent
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phenylisothiocyanate: sequentially removes each amino acid from the N terminus side (most common tech in labs)
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What is the relationship between what basic and acidic amino acids do to isoelectric points?
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Basic always increase pI.
Acidic always decreases pI. |
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Hydrophillic Amino Acids differ from their hydrophobic counterparts in terms of their charges how?
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Hydrophillic aa contain polar groups in the side chains. Because they are polar, they are capable of losing the H (hence are protic side chains). They can be charged.
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what are the structures of each of the following:
1. Amine 2. Amide 3. Imine 4. Hydroxyamine 5. Hydrazine 6. Oxime |
1. N single bond with C and H.
2. you know 3. N double bond with C 4. NH2OH 5. N single bonded to another N 6. N with a OH double bonded to C |
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What are the (4) factors that affect a compound's basicity?
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1. inductive effect
2. Steric hindrance 3. hydrogen bonding 4. solvation |
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Azide
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N3
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What would be the likely product from reacting ammonia with an alkyl hailde?
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Multiple substitutions - tertiary amines and such. Since methyl groups are electron donating.
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Gabriel Synthesis
- what is the structure - how do we activate it? |
see II p.167 to see the structure.
We need a stronger base to deprotonate it so it ll become a stronger nucleophile. (KOH) |
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What are the 7 ways of synthesizing amines
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1. Gabriel Synthesis
2. Azide Reduction 3. Nitrile Reduction 4. Amide Reduction 5. Imine Reduction 6. Hoffman Rearrangement 7. Curtius Rearrangment |
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Conformational Isomers
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Staggered (Gauche, Anti), and Eclipsed
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Cis and Trans are what kind of isomers?
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Diastereomers
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When we have two stereocentres, what does 1 switch indicate? 2 switches?
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1 switch: Dias
2 Switch: Enan |
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How does the energy diagram for a meso compound change?
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Energy diagrams are not symmetrical when there is chirality, however, since a meso is symmetrical, we have symmetry in the energy diagram.
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Name some activating/deactivating groups for para/ortho and meta.
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Activating: anything with a free pair of electrons/alkane groups (OH, OR, NH2)
Deactivating: anything with no free pair of electrons. (CO2, NH3, CN, NO2, CHO) |
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settle the B and the A bond for all sugars including the elusive fructose.
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B = ALWAYS the same side of the C6 Group!
A = ALWAYS the opposite side of the C6 Group! There are always two ways too look at a sugar - the way on the page or the reverse direction! |
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What is special about sucrose?
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The bond between glucose and fructose is 1,2 not 1,5 as you might expect from the other disaccharides with pyranoses.
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What is the general formula that determines if it is carbohydrate?
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Cn(H20)n
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