Organic Chemistry Flashcards
Which orbitals combine to form pi bonds?
One s and one p
Relative energies of the subshells
s < p < d < f
Tetravalent
Able to form bonds with 4 other molecules
Compare Bonding and Antibonding orbitals
Bonding orbitals occur when the signs of the separate orbitals’ wave functions are the same, they are lower energy than antibonding which occur when the signs of the wave functions are different.
Sigma bond
Occurs when an MO is formed by head-to-head or tail-to-tail overlap. Another name for single bonds
Pi bond
Occurs when two p-orbitals line up in parallel. Cannot exist without a sigma bond being present too. Individual pi bond is weaker than a sigma bond
Hybridization of C in alkenes.
How many of these hybridized orbitals are there and how many degrees apart are they spaces?
sp2 - because the third p-orbital is left unhybridized so that it can participate in the pi bond. 3 sp2 orbitals, spaced 120 degrees apart
Purpose of Hybridization
To make all of the bonds on the central atom equivalent to each other
sp hybridized orbitals
Spaced 180 degrees aparat. In triple bonds, two p-orbitals need to be left unhybridized to form the two pi bonds, so only one p-orbital and on s-orbital hybridize. They have 50% s character and 50% p character. Also occurs in Cs with double bonds on each side (like CO2)
Resonance structure
One possible distribution of electrons in a compound with conjugated bonds
Conjugation
Requires alternating single and multiple bonds in order to align a number of unhybridized p-orbitals down the backbone of the molecule through with pi electrons can delocalize. Increases stability
Mechanism of sp3-hybridization
“Promoting” one of the 2s electrons to the 2p_z orbital
Relative electrophilicity between CH3Cl and CH3OH
CH3Cl is a better electrophile because of the different leaving groups. Cl- is a weaker base than OH- (becuase HCl is a stronger acid), so Cl- in solution will be more stable than OH- in solution after the reaction occurs
Dichromate + secondary alcohol
Reaction results in a ketone. Dichromate is a strong oxidizing agent
Pyridinium chlorochromate
A weak oxidizing agent. Will react a primary alcohol to an aldehyde.
Why do SN1 reaction show first order kinetics?
Because the rate-limiting step only involves one molecule
PCC
Can oxidize primary and secondary alcohols because the central C can form additional bonds with oxygen while losing bonds to hydrogen. Weak oxidant (cannot take primary alcohols all the way to carboxylic acid)
Relative reactivity of alkanes in SN2 pathways
methyl > primary > secondary (tertiary does not react because steric hindrance is too great)
Relative reactivity of carboxylic acid derivatives
Anhydrides > carboxylic acids/esters > amides. Forms of higher reactivity can be reacted to form derivatives of lower reactivity but not the opposite direction.
Lewis Acids
Electron acceptors. Have a vacant p-orbital that can accept an electron pair
Lewis Base
Electron donors in the form of “extending” a coordinate covalent bond
Bronsted-Lowry Acids and Bases
Acids: H+ donors. Bases: H+ acceptors
Amphoteric
Molecules that have the ability to both accept and donate protons (act as both B-L acids and bases). Ex: water, Al(OH)3, HCO3-, HSO4-
Acid dissociation constant
Ka = [H+][A-] / [HA].
pKa = -log(Ka)
The larger the Ka, the stronger the stronger the acids (and the weaker the conjugate base)
pKa of “strong” acids
0 or below
alpha C and alpha H’s
C adjacent to the carbonyl C and the H’s bonded to it
4 Major Factors of Nucleophilicity
Charge: nucleophilicity increases with increasing electron density
Electronegativity: nuc decreases with increasing EN because atoms hold their e tightly
Steric hindrance: Bulkier molecules are less nucleophilic
Solvent: Protic solvents can hinder nuc by protonating the nucleophile or through H-bonding
Periodic Trend of Nucleophilicity
Nucleophilicity increases going down a group on the periodic table. Ex: I- is the most nucleophilic halogen in protic solvents because it is the conjugate base of a strong acid, so it least readily protonates, leaving it available to attack the electrophile
Effect of polar aprotic solvents on nucleophilicity (and period table trend)
Nucleophilicity increases going up a group in the period table. Ex: F- is the most nucleophilic halogen in aprotic solvents. This is because F- is the CB of a strong acid and there are no free protons to get in the way of it binding to an electrophile
Ranked electrophilicity of carboxylic acid derivatives
Anhydrides > carb. acids & esters > amides
Heterolytic reactions
Opposite of coordinate covalent bond formation. They are reactions in which bonds are broken and both electrons are given to one product. Examples include reactions with leavig groups
Good Leaving Groups
Weak (stable) bases. Conjugate bases of strong acids
SN1 reactions
- Leaving group dissociates, forming a carbocation (with is in a planar intermediate)
- Nucleophile attacks carbocation
Results in a racemic mixture
Rate limiting step of SN1 reactions
Formation of the carbocation (step 1)
SN2 reactions
Bimolecular nucleophilic substitution reactions. One step: backside attack of an electrophilic C and active displacement of the previously-bound leaving group. The less substituted the C, the faster the rate of reaction.
Stereospecific reaction: SN2
If the electrophilic C is chiral, configuration will be flipped from R to S (or vice versa) because of the backside attack by the nucleophile
Reagents for primary alcohol to carboxylic acid
STRONG oxidants: CrO3, Na2Cr2O7, K2Cr2O7
What makes a good oxidizing agent?
High affinity for electrons (O2, O3, Cl2), or unusually high oxidation states (Mn^7+ in MnO4-, and Cr^6+ in CrO4^2-)
Characteristics of good reducing agents
Low electronegativity and low ionization energy, also containing an H- ion (like LiAlH4, NaH, CaH2, and NaBH4)
LiAlH4 / LAH
STRONG reducing agent. Can reduce carb acids/ketohydes to alcohols, and can reduce amides to amines
Chemoselectivity
Preferential reaction of one functional group over reaction of another. Ex: a reducing agent will most readily react with the highest-priority functional group. Nucleophilic/electrophilic reactions will also take place at the highest-priority functional group because it is the likely location of the most oxidized C
Alternative alkyl substituents (know how to draw them)
t-butyl, neopentyl, isopropyl, sec-butyl, isobutyl
When ordering substituents alphabetically ___ factor in iso-, neo-, cyclo-, and ___ factor in di-, tri-, t-, etc.
do; do not
Common names for:
Methanal
Ethanal
Propanal
Formaldehyde
Acetaldehyde
Propionaldehyde
Geminal diols
Diols in which the two alcohols are on the same C
Vicinal diols
Diols in which the two alcohols are on two different neighboring Cs
Ketone suffix
-one
Aldehyde suffix
-al
Smallest possible ketone molecule
Acetone
Ester suffix
-oate
Anhydride suffix
-oic anhydride
Meso compounds
Compounds that have at stereocenters but are achiral due to an internal plane of symmetry. No optical activity
Relative configuration
Refers to configuratio of one chiral molecule compared to another
Absolute configuration
Refers to exact spatial arrangement of branches on a chiral center (R and S)
Maximum number of stereoisomers
= 2^n
Stereoisomers
Have the same formula and connectivity but differ in arrangement. Etiher configurational isomers or conformational isomers
Conformational isomers
Differ by rotation about a single bond. The molecules are the same, just instantaneously oriented differently
Configurational isomers
Can only be interconverted by breaking bonds
Enantiomers
Non-superimposable mirror images. Differ in R/S at every chiral center
Diastereomers
Non-mirror image configurational isomers. Different R/S at at least one but not all chiral centers
Epimers
Diastereomers that differ in R/S at only one chiral center
Types of strain in cyclic molecules
Angle strain, torsional strain, and nonbonded strain
Angle strain
Arises due to the bond angles deviating from ideal values because of stretching and compressing in ring
Torsional strain
Due to eclipsed/gauche conformation
Nonbonded strain
Van der Waals repulsions due to nonadjacent atoms or groups competeing for the same space. This is minimized in chair conformation when bulkiest groups are in equatorial position
Gauche configuration
The two largest groups are staggered, but only separated by 60 degrees
Totally eclipsed configuration
Two bulkiest groups in Fischer projection are overlapping
The presence of more alky groups on an alcohol ____ the acidity of the hydroxyl H because _____ .
Decreases; alkyl groups are electron-donating, which destabilizes the negative charge that results on the deprotonated oxygen. Unstable conjugate base = weak acid.
PCC
Pyridinium Chlorochromate. Reacts primary alcohols to form aldehydes and secondary alcohols to form ketones
Can tertiary alcohols be oxidized? Explain
They cannot be oxidized except under very harsh conditions because the hydroxyl carbon has no hydrogens to remove, so a C-C bond would have to be broken in order to create another bond with the alcohol
Cr(IV) as a reducing agent
Takes primary alcohols to carboxylic acids and secondary alcohols to ketones. Itself gets reduced to Cr(III). Exists in the forms of dichromate salts and chromate (CrO3), like Jones reagent
Jones oxidation
Fully oxidizes primary and secondary alcohols. Reagent is CrO3 with dilute H2SO4 in acetone.
Mesylates and Tosylates
-SO3CH3 and -SO3-C6H4-CH3, respectively. Replace the H on alcohols in order to make them into better leaving groups or protect them from undesired reactions
Protections groups introduced by reacting ____ with 2 equivalents of alcohol or a diol.
Method of removal
Converts aldehydes to acetals, and ketones to ketals. Deprotect by reacting with aqueous acid
Phenols + oxidizing agents ->
Quinones (2,5-cyclohexadiene-1,4-diones. Not always aromatic. Examples: Vitamin K1 (phylloquinone) and vitamin K2 (menaquinone)
Ubiquinone
AKA Coenzyme Q. Vital electron carrier in electron transport chain complexes I, II, and III. Reduced form is ubiquinol.
Forming geminal diols from ketohydes
Occurs in the presence of water. Happens slowly but can be accelerated by small amount of acid or base catalyst
Formation of hemiacetals and hemiketals from ketohydes
Occurs when one equivalent of alcohol is reacted with an aldehyde or ketone. OH group is retained on the former carbonyl carbon. Only one -OR group is added
Formation of acetal or ketal from ketohyde. Describe mechanism
An SN1 reaction catalyzed by an anhydrous acid. Occurs when two or more equivalents of alcohols are reacted with aldehyde or ketone. Mechanism involves formation of hemiacetal or hemiketal and then protonation of the hydroxyl group to make it into a good leaving group. Nucleophilic O of second alcohol then attacks carbocation.
Deprotection of acetal/ketal
Acid and heat are required to reform the aledhyde/ketone
Imine formation
Reaction of ketohyde with ammonia/ammonia derivative in which N replaces the carbonyl O. Classified as both a nucleophilic substitution reaction and a condensation reaction because a water molecule is lost.
Ammonia derivatives that can engage in imine formation
Hydroxylamine, hydrazine, semicarbazide
Enamines
The product of imine tautomerization. The double bond now resides between the C attached to the N and one of its R groups.
Formation of cyanohydrins from ketohydes
Nucleophilic attack on ketohyde by HCN to form the tetrahedral cyanohydrin. Highly stable because of new C-C bond
Reagents that oxidize aldehydes to carboxylic acids
KMnO4, CrO3, silver(I) oxide (Ag2O), and hydrogen peroxide (H2O2)
Reagents that reduce of ketohydes to alcohols
Hydride compounds like LiAlH4 (LAH) and NaBH4 (milder, but be careful of BH3 reaction with double bond)
DNA Methylation
Silences genes. Heterochromatin (transcriptionally silent) is heavily methylated.
trp operon
Repressible operon that stops being transcribed in the presence of tryptophan.
aminoacyl-tRNA synthetase
Transfers activated amino acid to the 3’ end of the correct tRNA to be brought to the ribosome. This attachment requires two high energy bonds from ATP
The template strand of DNA is also called the ____/____ strand and is ______ to the hnRNA
Antisense/noncoding; complementary (antiparallel)
hnRNA
Heterogeneous nuclear RNA: primary RNA transcript initially formed by transcription. Precursor to mRNA
The nontemplate strand of DNA is also called the ____/____ strand and is ______ to the hnRNA
Coding/sense; identical (but replace Ts with Us)
RNA Polymerase I
Located in the nucleolus and synthesizes rRNA
RNA Polymerase II
Located in the nucleus and synthesizes hnRNA and some snRNA
RNA Polymerase III
Located in the nucleus and synthesizes tRNA and some rRNA
Steps of Transcription
DNA-dependent RNA polymerase searches the template strand for a promoter region, then binds to the TATA box (about 25 bases upstream of the start codon) in the promoter region (aided by transcription factors). No primer is required for RNA polymerase to bind. RNA polymerase begins elongation, reading the template strand from 3’-5’, synthesizing hnRNA in the 5’-3’ direction. No proofreading is performed during.
Spliceosome and role in posttranscriptional events
A large protein complex in the nucleus. Contains snRNA that couple with snRNPs (proteins). snRNA/snRNP complexes recognize the 5’ and 3’ splice sites of introns, and splice them out in the form of a lariat
Lariat
Lasso-shaped structure created by spliceosome in excising introns from hnRNA
Small nuclear ribnucleoproteins
snRNPs - couple with snRNAs to excise introns
5’ cap
Protects mRNA from degradation in the cytoplasm. Specifically is a 7-methylguanylate triphosphate cap
Poly(A) tail
Gets added to the 3’ end of mRNA to prolong degradation. As soon as the mRNA hits the cytoplasm, it starts getting degraded from the 3’ end, so the longer the poly(A) tail, the longer the mRNA survives.
Peptidyl transferase
Enzyme in the ribosome that catalyzes formation of the peptide bond between the amino acids at the A and P sites
Termination of Translation
Triggered by the entrance of a stop codon into the A site of the ribosome, release factor protein binds to the termination codon. Causes a water molecule to be added to the polypeptide chain. This hydrolyzes the entire polypeptide chain from the ribosome.
Chaperones (proteins)
Assist in the folding of a newly-synthesizes polypeptide chain into a functional protein, with the help of other folding mechanisms
Posttranlational modifications
Cleavage, assembly to form quaternary structure, covalent modifications like carboxylation, phosphorylation, glycosylation, and prenylation (addition of lipid groups)
Structure of an operon
From 5’ to 3’:
Regulatory gene — Promoter site (where RNApol binds) — Operator site —- Structural gene (encodes prot.)
Binding site of repressor on operon
Operator site
What does the regulator gene encode for on an operon?
The repressor protein
Inducible operon mechanism
As concentration of the inducer molecule increases, the operon pulls more and more repressors off of the operator site, allowing transcription
lac operon, CAP, and cAMP
lac is an inducible operon that is active in the presence of lactose. When glucose levels in the body fall, cAMP levels rise, and cAMP binds to CAP (catabolite activator protein). CAP binds to the promoter region of lac, increasing transcription. Ex of a postiive control mechanism
Repressible operon mechanism
Repressor protein is inactive at rest, allowing transcription until bound by a corepressor which causes the repressor to become activated and bind to the operator, causing transcription to stop.
trp operon and its corepressor
A repressible system that synthesizes tryptophan for the body until the corepressor stops it. Tryptophan acts as the corepressor because when levels in the body are high from food/supplements, the body does not need to make a lot of its own, so tryptophan binds to the repressor, causing it to become activated and bind to the operator and stop synthesis of tryptophan
DNA response element
A DNA sequence that binds to specific transcription factors to help transcription machinery at their DNA-binding domains.
Gene amplification
Achieved either through gene duplication or enhancers
Enhancers
Collections of DNA response elements that control for one gene’s expression in response to multiple signals. Large space between the enhancer and the promoter region forces the mRNA to form a hairpin loop to bring the elements together. Can even be located on an intron. Ex: cAMP binding to CREB, cortisol, and estrogen
Histone acetylases
Involved in chromatin remodeling in such a way as to increase transcription. They work by acetylating lysine residues, thus decreasing the positive charge and weakening the interaction of the DNA with the histone, opening up the chromatin making it more susceptible to transcription machinery. Histone deacetylases undo this and decrease gene expression
DNA methylation
Linked with silencing gene expression. It is the addition of methyl groups to C and A nucleotides. Heterochromatin is more highly methylated than euchromatin.
Michael Addition
An enolate (carbanion that was activated by a base) attacks an alpha-beta unsaturated bond of a 1,3-dicarbonyl, forming a new bond
The _____ tautomer is the nucleophile in aldol condensation, and _____ tautomer is the electrophile.
enol; keto form
Conditions required for an aldol to undergo elimination.
What product does this produce?
Stong base and high temperatures.
Product = alpha-beta unsaturated carbonyl
Retro-aldol reaction
Used for breaking the bonds between alpha and beta carbons on an aldol, forming two ketohydes
Conditions that favor thermodynamic enolate
Low temps, small and weak bases, reversibility
Conditions that favor kinetic enolate
High temps, irreversibility, strong and bulky bases
Define “dimer”
Why do carboxylic acids tend to form them?
def: pairs of molecules held together by two hydrogen-bonds.
Carb acids tend to form them because the Os in both the carbonyl group and the hydroxyl group can participate in H-bonding. Makes them have very high MPs and BPs
Lactams
Cyclic amides
Lactones
Cyclic esters
Carboxylic acid + ammonia/amin –>
Amide
Carboxylic acid + alcohol –>
Ester
Carboxylic acid + carboxylic acid/derivative –>
Anhydride
Spontaneous decarboxylation
Happens to beta-dicarboxylic acids and other beta-keto acids when heated. CO2 is lost. Reaction proceeds through a 6-membered cyclic intermediate
Saponification
Fatty acid (long-chain carboxylic acid) + strong base = soap (a carb. acid salt)
The alpha hydrogen of a carboxylic acid is _____ acidic than the hydroxyl H
Less
T/F: NaBH4 can reduce carboxylic acids to aledhydes
FALSE: NaBH4 is not strong enough to react with carboxylic acids at all. It can only reduce aldehydes, ketones, and acid chlorides
beta-lactams
Cyclic amides that have a bond between the beta carbon and the N
Amides have the same or _____ boiling points than carboxylic acids
lower
Naming of esters
Prefix is the esterifying group (the substituent bonded to the O). Ends in -oate
Fischer esterification
Condensation of carboxylic acids and alcohols under acidic conditions
Anhydrides have ____ boiling points that their carboxylic acid counterparts because of…
Higher - because of their much greater weight
Induction
Refers to the distribution of charge across sigma bonds
Conjugation
Alternating single and double bonds or lone pairs. Implies that all atoms in these bonds are sp2 or sp-hybridized, so they have unhybridized p-orbitals. Pi electrons can delocalize through resonance and stabilize the molecule
Enones
alpha,beta-unsaturated carbonyls
How to form carboxylic acids from anhydrides
Expose them to water
Transesterification
Alcohol + ester –> new ester
Hydrolysis of amides
Requires acidic catalyst
All naturally occurring amino acids are the _-isomer, except for _____.
All optically active amino acids have __ configuration, except for ___, because…
L-isomer, except for Glycine (optically inactive, non-chiral)
S configuration, except for Cys because the sulfur in the side chain changes priority of the branches off the chiral center
Zwitterion
A molecule with separated charges, but a net charge of zero. Amino acids form these.
Amphoteric
Able to act as both an acid and base
Nonpolar nonaromatic amino acids
Glycine, proline, alanine, valine, leucine, isoleucine, methionine
Nonpolar aromatic amino acids
Tryptophan, phenylalanine, and tyrosine
Polar amino acids
Serine, threonine, asparagine, glutamine, and cysteine
Negatively charged amino acids
Acids!
Glutamic acid and aspartic acid
Positively charged amino acids
Basic!
Histidine, lysine, and arginine
Strecker synthesis
Forms and a racemic mixture of an amino acid, starting with an aldehyde, NH4CL, and KCN. Mechanism:
Ammonia attacks the carbonyl C, forming an imine. CN- ion from KCN attacks the imine C to form a nitrile group, for an overall aminonitrile. Nitrile N is then protonated and then water attacks the nitrile C to form an imine. The imine is attacked by another water molecule, forming a carbonyl, kicking off ammonia, thus creating carboxylic acid functionality (final step can be sped up by acid and heat)
Gabriel Synthesis / malonic ester synthesis
Synthesis of a racemic mixture of an amino acid from phthalimide diethyl bromomalonate, via:
- Two SN2 reactions (second one introduces desired R group)
- Hydrolysis (with strong base and heat)
- Decarboxylation (requires acid and heat)
Phosphoric acid
AKA inorganic phosphate, or P_i. Forms the high energy bonds of ATP and is found in the phosphodiester bonds of DNA backbones
Pyrophosphate
PP_i. Formula is P2O7^2-. It is released from the DNA backbone when a new nucleotide joins the growing strand. It is highly unstable in aq, so it hydrolyzes to form 2 P_i, both of which can be recycled to form ATP
Organic phosphates
Those in ATP, GTP, and in DNA because a phosphate group bonded to a C molecule is present
Why is phosphoric acid a good buffer?
It has three hydrogens with pKa values that span nearly the entire pH scale
T/F: Both Gabriel and Strecker Syntheses result in optically active products
FALSE. Neither of them do because they both result in a racemic mixture
In Gabriel Synthesis, phthalimide serves as the _____.
nucleophile
Wich small molecule is released when a new nucleotide is added onto a growing strand of DNA?
Pyrophosphate (PP_i)
Most dissolutions are ___thermic, although dissolution of gas into liquid is ______.
Endothermic; although solvation of gas into a liquid is exothermic
Complex ions / Coordination compounds
Referred to as ligands. Composed of metallic ions bonded to various neutral compounds. Formation of complex ions increases solubility of otherwise insoluble ions
Lowering the temperature of a liquid ____ (favors or inhibits) solubility of a gas in the liquid.
favors
Endothermic solvation
Favorable at high temperatures. Characterized by the interactions between the solvent and solute being weaker than the interactions between the solvent itself prior to solvation. Most solutions are this type
Ideal solution
When the overall strength of the interactions between solvent and solute are approximately equal to those originally between the solvent particles. Enthalpy change approximately equal to zero
Threshold of a solute being considered “soluble”
solubility of .1 M or greater
Solubility
The maximum amount of a substance that can be dissolved in a particular solvent at equilibrium
Chelation
When the central cation can be bonded to the same ligan in multiple places. Generally requires large organic ligands than can double back to form a second bond with the central cation. Often used to sequester toxic metals (lead, arsenic, mercury, etc.)
Molality
Moles of solute per kg of solvent
Normality of a solution
Equal to the number of equivalents of interest per liter of solution. e.g. 1 mole of MnO4- in acidic solution can accept 5 electrons, so a 1 M solution would have a normality of 5 N, but in basic solution, it can only accept 1 e, so normality would be equal to 1
Solubility product constant for solvation reaction: A_m-B_n (s) -> m A^n+ (aq) + n B^m- (aq)
K_sp = [A^n+]^m * [B^m-)^n
Using equilibrium (saturation) concentrations
Ion product (IP)
The same calculation as K_sp, but using the instantaneous concentrations of products at a given time
IP > K_sp
IP
IP>K_sp –> supersaturated (only possible by heating the solvent, dissolving, and then cooling)
I< K_sp –> unsaturated
Formation/stability constant of complex ions
Equilibrium constant of formation of a complex ions from a mixture of solutions. Much larger than K_sp
Common ion effect
The decrease of a salt’s solubility in a solution that already contains one of its constituent ions. Basically LeChat’s Principle in action
Colligative properties
Physical properties of solution that are dependent on the concentrations of dissolved particles but not on the dissolved particles’ identity. They include: vapor pressure, BP elevation, FP depression, and osmotic pressure.
Raoult’s Law of Vapor Pressure Depression
As solute is added to a solvent, vapor pressure of the solvent is decreased proportionally.
P_A = X_A * P_A~
where P_A is the vapor pressure of solvent A, X_A is then mole fraction of solvent A in solution, and P_A~ is the vapor pressure of pure solvent A.
Ideal solution obey this law
BP elevation equation due to solvent
delta T_b = iK_bm
i: van’t Hoff factor = number of particles into which a compound dissociates
K_b: constant for the solvent that will be provided
m: molality of the solution
Boiling point of a solution increases as solute is dissolved. This is also apparent in the decrease in vapor pressure because it shows that more energy is needed to overcome IMFs between solvent particles
FP Depression of solution
Presence of a solute causes a decrease in FP because the “extra” particles interfere with arrangement of the solute particles in crystal form
delta T_b = iK_fm
Osmotic pressure
The “sucking” pressure generated by hyperosmotic solutions
P_osmotic = iMRT
where M is molarity, R is gas constant, i is van’t Hoff factor, and T is temp.
Increased molarity in a solution will cause an increased osmotic pressure into that solution because it is “wanting” more water
What kind of solutions do not obey Raoult’s Law?
Solutions in which the interactions between the solute and solvent are NOT roughly equal to the interactions between the separate components in their pure states.
Which kind of solutions best obey Raoult’s Law regarding vapor pressure of solutions?
Mixtures in which the solvent-solvent, solvent-solute, and solute-solute interactions are very similar
Effect of complex ions on solubility
Complex ion formation essentially consumes components of the solute, motivating further dissociation by LeChatlier’s principle
Spectroscopy
In which major medical imaging tool is it essential?
Measures the energy differences between the possible states of a molecular system by determining the frequencies of electromagnetic radiation absorbed by the molecules.
MRI - it actually measures the H-NMR spectra of water molecules in different environments in the body
IR spectroscopy
Measures molecular vibrations - can be seen as bond stretching, bending, or combinations of different vibrational modes.
What type of molecules do not show up on IR spectroscopy? Why?
Symmetrical - because they have no dipole moment, and absorptions occur from vibrations that occur due to changes in dipole moment.
Symmetrical bonds also do not show up in IR spec because they have no dipole moment (ie bonds between two atoms of the same element)
Peak of -OH on IR spec (both alc and carb acids)
Broad peak
Alcohols: 3300 1/cm
Carb acids: 3000 1/cm
Higher electron density around a bond correlates with _____ wavenumber
Higher
ex: carboxylic acids pull some of the electron density away from the OH bond, so the carb acid peak occurs at a lower wavenumber than OH alone
N-H peak on IR spec
Around 3300 1/cm, just like alcohol except this one is sharp whereas alcohol’s is wide
Carbonyl peak on IR spec
Sharp peak at 1700 1/cm
What does IR spec plot measurements in?
Percent transmittance (the amount of light that passes through the sample and reaches the detector) vs wavenumber
Equation for wavenumber
Wavenumber = 1/wavelength
Aliphatic
Types of carbon-containing compounds that are open-chains, not aromatic rings
What types of compounds does UV spec best study? Why?
Conjugated compounds with double bonds and/or lone pairs because the pi electrons present can be excited by the UV light. With this higher energy, the compounds can absorb longer wavelengths.
“Downfield” on the x-axis of NMR graphs refers to which end of the axis?
The left
Axes of NMR
Frequency vs. absorption of energy (“chemical shift” in units of parts per million [ppm])
What type of spectroscopy does MRI utilize?
Proton-NMR
If a certain set of H’s in a compound is relatively deshielded, where will they lie on the NMR spectra in comparison to more shielded H’s?
They will be further to the left, further from the TMS peak (higher ppm, higher absorption of energy)
What is meant by protons being “deshielded” from a magnetic field and in what bonding situations would this arise?
This means that H’s are bonded to an electronegative atom that is pulling away electron density from the H, thus taking away the proton’s “shield” from the applied magnetic field.
What does a doublet mean on NMR?
It means that the H or group of H’s that are represented by the doublet are bonded to a C that is adjacent to another C also bonded to one H.
Do not include protons that are bonded to O or N
Coupling constant
J: Magnitude of splitting of a peak in NMR measured in Hz. This magnitude is caused by other atoms in the molecule
Peak indicating protons attached to sp3-hybridized C in H-NMR
between 0 and 3 ppm
Peak indicating protons attached to sp2-hybridized C on H-NMR:
4-6 ppm
Peak indicating protons attached to sp-hybridized C on H-NMR
2-3 ppm
Peak indicating protons on an aromatic ring C in H-NMR
6.5-8 ppm
Peak indicating H on an aldehyde’s C in H-NMR
9-10 ppm
Peak indicating H on carb acid C in H-NMR
10.5-12 ppm
Is Carbon-12 useful in NMR? Why or why not?
It is not because it has no magnetic dipole moment,
n + 1 rule for H-NMR
Then number of peaks corresponds to the number of protons that are 3 bonds away from the proton represented by the peak plus one
Describe the movement of electrons after absorption of UV light
An electron is excited from the HOMO to the LUMO
Immiscible
Describes a solvent that has two layers that do not mix
When performing an extraction with a separatory funnel, which solvent gets drained first?
The denser of the two layers
Distillate
The liquid with the higher boiling point in distillation
Condensate
The liquid with the lower boiling point in distillation
Superheating
Occurs when a liquid is heated above its boiling point but is not evaporating because it is unable to overcome the atmospheric pressure and surface tension
Effect of vacuum distillation on boiling point
Decreases BP because the vacuum decreases ambient pressure
Fractional distillation
Utilizes a fractionation column, the surface area of which is increased by the presence of steel wool or glass beads. Used to separate liquids with boiling points that are different by less than 25 degrees C.
Properties that can be be used to separate compounds in chromatography
Polarity(!!), size, charge, and antibody-ligand binding.
Stationary phase examples for polarity-based chromatography
Silica gel (highly polar, used in TLC), cellulose (in paper chromatography)
Which phase is polar in reverse-phase chromatography?
Mobile phase
Retardation factor (R_f) in TLC
R_f = distance spot moved / distance solvent front moved
Adsorbent in column chromatography
The silica or aluminum beads that fill the column and allow separation
Which compounds elute first in size exclusion chromatography?
Larger compounds will elute first because they cannot fit into the tiny pores, so they go around the beads.
Gas chromatography
Chromatography in which the eluent is a gas and the adsorbent is a crushed metal or polymer inside a 30-foot column. The injectable compounds (sample) must be volatile, meaning low melting point, sublimable solid or vaporizable liquids
Mass Spectrometry
Ionization and fragmentation of a compound of interest, and then running the fragments through a magnetic field, thus separating them by a mass-to-charge ratio. The total molecular weight can be determined, or the relative concentrations of the different fragments can be calculated and compared against reference values to identify the compound.
Solvents with _____ R_f values elute first
Higher (because this indicates that they travel a greater fraction of the total distance traveled by the mobile phase)
Acidic extraction
Separation method in which an acid species is removed using a base
T/F: Anomers are a form of epimer
True
Ketone + primary amine =
Imine
Ketone + secondary amine =
Enamine
Claisen Condensation
Condensation of two esters, resulting in a beta-keto-ester that is stabilized by resonance as the alpha C is commonly deprotonated
Dieckmann Condensation
An intramolecular Claisen condensation. Reactant: a diester; Product: a cyclic beta-ketoester
Amine + Carboxylic Acid Anhydride –>
Amide + Carboxylic acid
