Final Flashcards
What makes a compound organic?
If it is composed of carbon.
Define Natural Products
Molecules that are made by nature and are naturally occurring in our environment.
Are chlorophylls and Beta Carotene natural products?
Yes
What is the responsibility of chlorophyll?
Responsible for the green color of plants and the absorption of light to turn CO2 and water into chemical energy. (photosynthesis).
What is the main difference between chlorophyll and hemoglobin?
The central atom making their structure. Chlorophyll has magnesium in the center and hemoglobin has iron in the center.
How is chlorophyll beneficial to human health?
It can swap out magnesium for iron, converting to hemoglobin.
List some important things about beta Carotene.
It is the compound that gives carrots its orange color and is found in vegetables such as kale, spinach, and asparagus. Has anti-oxidative properties, is an anti-aging molecule, and fights oxidative stress.
Define Chromatography
General term that covers separation methods that utilize physical properties of the solutes in a mixture and the solvents used to separate them.
What is the main purpose of thin-layer chromatography?
To see substance is pure or if its consisted of multiple things.
What are the components of TLC?
The stationary and the mobile phases. The stationary phase is made of adsorbent material, competing with the mobile phase for the attraction of individual solutes. Thin plate of silica gel acts as the stationary phase. The mobile phase is made up of a solvent or a combination of solvents that vary in polarity.
Explain how TLC works.
As mentioned, it is made up of the stationary phase and the mobile phase. The stationary phase is the silica gel that is polar. The mobile phase is a solvent or a combination of solvents that vary in polarity. Polar solutes will move shorter along the plate since they have a strong attraction for the stationary phase. On the other hand, less polar solutes will travel further along the plate.
What does it mean for a sample to be resolved?
When two or more components can be separated.
Define Solvent Front
Where the solvent stopped traveling when the TLC plate is removed from the solvent.
By looking at a TLC plate, how could you tell if the substance is pure?
If there are multiple spots that resulted, then the substance is impure (consisted of multiple parts).
How do polar/non-polar compounds travel in the TLC plate?
The more polar the substance, the less it will travel in the TLC plate. The more non-polar it is, the more it will travel UP the TLC plate.
Define Retention Factor and what it indicates.
Rf= distance to the middle of the spot/distance to solvent front. The higher the Rf value, the more it interacted with the mobile phase (more non-polar). The lower the Rf value, the more it interacted with the stationary phase.
What is the relationship between Rf Values and Polarity?
Inverse.
Define Column Chromatography
The most common technique for purification. Silica gel acts as the stationary phase and the solvent/eluent added acts as the mobile phase. In column chromatography, the direction of solvent flow is from top to bottom, opposite of TLC: both the compound and the solvent are added to the top, which flow DOWN the column. So, the top layer is made of the solvent/compound add the bottom layer is made of silica gel.
What are the regions of visible light?
400-700nm; ROYGBIV. Red corresponding to 400nm, and violet corresponding to the violet.
What’s the relationship between wavelength and energy?
Inverse
What makes a molecule conjugated?
It has to have at least 2 pi bonds.
What’s the relationship between the observed color and the absorbed color?
The observed color is opposite on the wheel compared to the absorbed color.
What is rotovap primarily used for?
To remove solvents quickly from the extract that contains the organic compound dissolved alongside the organic solvent. LOWER PRESSURE ABOVE THE LIQUID TO ALLOW IT TO BOIL BELOW ITS NORMAL BOILING POINT.
In the 2nd lab, the addition of what solvent led to the formation of the yellow band?
Hexanes
The formation of a yellow band in column chromatography is indicative of what?
The separation of Beta Carotene.
The formation of a green band in column chromatography is indicative of what?
The separation of chlorophylls.
The addition of which solvent led to the formation of a green band?
30% Acetone/hexanes.
In the second lab, how were beta carotene and chlorophylls isolated/extracted?
They were isolated via solid-liquid extraction (vacuum filtration). They were separated via column chromatography to see their color properties.
What is the relationship between conjugation of a molecule and the light that it absorbs?
The more conjugated the molecule, the higher wavelength light is absorbs.
In the 2nd experiment, which band eluted first from column chromatography?
The yellow band, meaning beta carotene eluted first.
You have been provided UV/Vis spectra for β-carotene and chlorophyll A/B. Based on their absorbances, which product eluted first? Which product eluted second? Using the data provided, explain how you came to your conclusions.
We know that polar compounds have intense absorptions of light frequency, which can be seen in the absorbance diagram of chlorophyll. Being the more polar compound, chlrophyll eluted 2nd. The non-polar compound, beta carotene, eluted first.
Consider the conjugated systems of the chlorophylls and hemoglobin. Suggest a reason for why hemoglobin is red-shifted compared to the chlorophyll b, which appears yellow (chlorophyll a has a more distinct green color).
Chlorophyll A is more conjugated than B, leading to it absorbing light at a higher wavelength.
Define Stereoisomers
Molecules that have the same formula, but different spatial arrangements.
What are the conformational isomers?
Eclipsed and Staggered
Which of the conformational isomers are more stable? Why?
Staggered is more stable (lower in energy). In the eclipsed conformation, there is torsional strain, leading to an increase in the energy.
Define Torsional Strain
The strain imposed by interactions in the eclipsed state. (
What is the major type of strain present in cyclopropane and cyclobutane?
Angular strain
What structure does cyclobutane adopt to avoid angular strain?
Puckered
What structure does cyclopentane adopt to alleviate strain?
Envelope
Which of the cycloalkanes is the least strained? Why?
Cyclohexane. Because it can adopt the chair conformation to minimize torsional strain.
How is an axial position pointing?
Straight up or down.
From wedges and dashes, how could you tell if something is going to be in the equatorial or axial position?
Wedge is up in the chair conformation and dash is down on the chair conformation
What happens to cycloalkanes in terms of experienced strain after they surpass cyclohexane?
They become more strained due to the experiencing of transannularstrain, arising from the steric clash of substituents from the opposite side of the ring.
Which force field can generally be applied to most of the molecules for?
GAFF
Define Geometry Minimization
A process that finds the lowest energy conformation.
How many protons are involved in transannular strain on each face of cyclooctane? Cycloheptane?
3.
What makes a carbon chiral?
Sp3 hybridized and attached to 4 different groups.
Define Achiral
2 molecules are the same and are superimposable.
Define Enantiomer
Non-superimposable mirror image of a molecule.
How do you determine the configuration of a molecule?
Priority assignment based on atomic #. Make sure that the lowest priority group is pointing away. If not, then what looks to be R is S and what looks to be S is R. Clockwise —> R; Counterclockwise —> S
How do you draw the constitutional isomers for something?
You calculate the HDI: (2C+2-H(OR X)+N))/2. The result gives you a number. It can either be a pi bond, ring, or a mixture of both. Adjust accordingly.
What is another name for aspirin?
Acetalicyclic acid.
What is another name for Tylenol?
Acetaminophen
What are some examples of solid-liquid extraction?
Brewing a cup of coffee, brewing a cup of tea, extracting B carotene and Chlorophylls A/B from spinach.
When are two liquids said to be immiscible?
When they have very different polarities.
For the purposes of this class, what is the aqueous layer going to mainly be consisted of?
Water
What will the organic layer react with?
Organic compounds will interact with the organic layer more than the aqueous layer.
How do you extract an organic compound out of water?
By mixing it with an organic solvent. Since the 2 layers are immiscible, the organic compound will find its way out of the water.
To extract a water-soluble compound out of an organic mixture, use ______.
Water
Define Washing
When you get rid of something undesirable.
What is the difference between extraction and washing?
With extraction, you end up with something you want and with washing, you are getting rid of something undesirable.
Define Acid-Base Wash
Upon having some unwanted acid or base in the organic layer, some acid/base can be added accordingly to get rid of the unwanted portion.
When there’s something that we want, we _____ it.
Extract
When there’s something that we want to remove, we ______ it.
WASH
Define Crystallization
A technique for purifying solid compounds. You dissolve the solid solute in a hot solvent which breaks apart the crystal lattice. Upon cooling, the crystal lattice begins forming without the impurities.
When recrystallizing with a single solvent, what is the ideal case for solubility?
It should be more soluble in higher temperatures and less soluble in lower temperatures.
When doing recrystallization, what is something we want to keep mental note of?
To add a minimum amount of hot solvent. When too much solvent is used for the recrystallization process, it’s possible that crystals will not form during cooling.
When adding dichloromethane to the mixture containing aspirin, tylenol, and caffeine, which of the solids did not dissolve? Why?
Tylenol. Because it was insoluble in DCM.
Within the separatory funnel, what’s present in the organic and the aqueous layer respectively?
Top is aspirin (aqueous layer) and the bottom is caffeine (organic layer with DCM).
What’s the underlying factor that allows for aspirin to be separated from caffeine?
Caffeine doesn’t react with NaOH, whereas aspirin does.
How can caffeine and aspirin be regarded respectively?
Organic Base and an Organic Acid
What is the purpose of adding HCl to the solution containing aspirin?
To protonate acetalycyclic acid,
You’re performing an aqueous extraction, and you forget which layer is the organic layer and which is the aqueous layer. What is the best way to solve this problem?
Add a small amount of sodium sulfate - if it dissolves, the layer is water.
What happened to aspirin when NaOH was added to the separatory funnel?
It turned into water soluble sodium salt, making it go into the aqueous layer.
In Part C, why does a solid precipitate form when a solution of strong acid was added? Explain what is occurring and include the arrow-pushing mechanism.
Because when the water soluble salt is acidified, it’s no longer soluble, leading to it precipitating.
Do all substances have a unique melting point range?
Yes
What will the presence of contaminants do to the melting point range?
Expand/compress it by a couple degrees.
How is the melting point range determined?
Starts from when the substance begins melting to when it’s fully melted.
Saturation at High Temperatures=?
Supersaturation at Low Temperatures
Define Scratching
Using a stirring rod to scratch the sides of a flask to promote nucleation (the birth of new crystals from which crystal growth occurs).
Define Seeding
When we know the identity of what we’re recrystallizing, we can add a small amount of it to the solution, helping promote growth.
What is the difference between precipitation and crystallization? What are the reasons that precipitation can happen?
Precipitation is when the solid substance unexpectedly comes out of the solution, still remaining impure. This can happen due to a multitude of reasons: not allowing the solution to GRADUALLY cool, instantly transferring it into a cold bath.
Specifically, explain what happened when NaOH was added to the separatory funnel.
When NaOH was added to the funnel, acetalycyclic acid was deprotonated, leading to the formation of water soluble sodium salt which allowed it to interact with the aqueous layer. Afterwards, HCl was added to protonate the salt, leading to the reformation of the acid.
Why are heated solvents used to initially dissolve the solvents?
Because they dissolve better in hot solvents, become supersaturated upon cooling, and they allow for a minimum of solvent to be used.
How does the inadequate removal of solvents affect the melting point analysis?
Depresses the melting point, and expands the melting range. When solvents aren’t adequately removed, they introduce impurities.
Why are multiple solvents sometimes used for recrystallization?
Because sometimes, the solvent is too polar and will not allow the lattice to cool when placed in ice. In other cases, it might not be polar enough to dissolve the compound. So, a mixture is used to ensure ideal conditions.
How does the presence of impurities affect the melting point of something?
It DEPRESSES the MELTING POINT and EXPANDS the melting point range.
What will happen if more than the minimum amount of hot solvent is used?
The yield for recrystallization will be lower.
Why do we use eluents that vary in composition/mixture in TLC analysis?
Because they will have different polarities, being able to react with compounds that vary in polarity accordingly.
Do twist boats have more eclipsing interactions or boat conformations?
Boat conformations
Are there any eclipsing interactions present with the chair conformation?
No
What is the optimal bond angle between 3 atoms?
109.5
When does angular strain arise?
When the bond angle deviates from the optimal bond angle.
Rank the chair, twist boat, and boat structures based on increasing stability?
Chair, twist boat, and boat.
Is it possible for C6H12 to adopt a planar conformation?
No, it’s not. To adopt a planar conformation, the angle would have to be 120.
Is the aqueous layer always under the organic layer?
No
What happens if a compound decomposes upon heating in crystallization?
We must do recrystallization with 2 solvents, where it is soluble in one and insoluble in another.
Define Nucleophiles
Functional groups with high electron density. Can be pi bonds and lone pairs as well.
Define Electrophiles
Functional groups with low electron density. Partial positive charge is characteristic of them.
What solvents are best for SN2 reactions?
Polar Aprotic
Why are polar protic solvents not good for SN2?
Since they have N,O,F and halogens bonded directly to hydrogen, they will cause the hydrogens to have a partial positive charge, making them react with the nucleophile. As a result, the nucleophile would become less reactive since it’s becoming more stable.
Define Polar Aprotic Solvents
Solvents that do not have N,O,F, or halogens directly bonded to H
What sort of substitution do SN1 reactions favor?
More substituted alkyl halides/alcohols.
What sort of substitution do SN2 reactions favor?
Less substituted substrates.
What effect does the strength of the nucleophile have on favoring SN1/SN2 reactions?
Weak nucleophiles tend to favor SN1 reactions and strong ones tend to favor SN2.
In the 7th experiment, what was used as the nucleophile?
NaI
What are the precipitation products of the SN2 reactions conducted?
NaBr and NaCl
What were the conditions for SN2 and SN1 reactions?
NaI dissolved in acetone and AgNO3 dissolved in Ethanol
Explain the mechanism that happened with the SN1 reaction.
LLG- Formation of Carbocation-NA by ethanol- PT by NO3.
What are other examples of Polar Protic Solvents?
Methanol/Water
What are other examples of polar aprotic solvents?
DMSO, Acetonitrile
Why are polar protic solvents good for SN1 reactions?
Because they make hydrogen bonds with the leaving group in the transition state, making it more stable.
Define Distillation
A technique used to isolate volatile and low boiling compounds. A liquid is heated, turned into vapor, and condensed back into liquid. Upon vaporization, the impurities are removed.
Under what conditions are elimination reactions favorable?
When there’s a strong base present.
What are the products of 2-methylcyclohexanol and 4-methylcyclohexanol reacting with H3PO4?
C7H12 and H2O
How are alkenes named?
The numbering starts at the carbons with the double bond. Has to be done in a way where the attached substituent is in the lowest numbered position.
Define Gas Chromatography
A technique that separates a mixture of molecules in the gas phase by using hydrogen or helium as the mobile phase.
What are some key differences between Liquid and Gas Chromatography?
Liquid Chromatography: Separates liquids in a mixture- Liquid Solvent Mobile Phase- Column typically in inches- Separation based on polarity.
GC: Separates gases in a mixture-Gaseous mobile phase (helium/hydrogen)- Column is very long (60m)- Separation based on boiling point.
Based on a gas chromatograph, how could you tell if something has the highest boiling point?
When it has the greatest area under the curve.
How do compounds with lower boiling points come out from gas chromatography?
The lower the boiling point, they faster they will come out.
What does the area under each curve of the gas chromatogram tell us?
How much of the substance is abundant.
Explain the elimination reactions that took place with the methycyclohexanols.
PT from OH to H3PO4, LLG of hydronium, OH2 acting as base leading to pi bond formation and LLG.
What’s the difference between CHO and COH?
CHO is an aldehyde and COH is an alcohol group
What are the substituent groups attached to chlorophylls?
Aldehydes and Alcohols
What makes chlorophyll more polar than beta carotene?
The presence of alcohol and aldehyde functional groups. Additionally, the presence of oxygen allows for the formation of H Bonds.
With elimination reactions, what do polar protic solvents favor? Why?
E1 reactions. Because they stabilize the carbocation intermediate.
