General CHemistry
Name the following hydrocarbons:
Draw the following hydrocarbons:
2,3-dimethylpent-1-ene
2-methyloct-4-yne
2,3,4-trimethylhexane
3-ethyl-2-methylheptane
Useful Links and Resources:
Sharemol is a web app built by CHEM 165's very own TF Facheng Guo. You can input a 2D structure in order to view a rotatable 3D model. This would be particularly good for looking at stereochemistry and chirality, especially if you don't have a model kit.
Click below to navigate to Yale's ITS Software page, where you can download ChemDraw for free. ChemDraw is the industry standard for making figures like the ones above. It has a naming feature if you click Structure > Structure to Name (or the inverse, Name to Structure if you want to input a name to generate the structure). This will help you quickly see the answers to questions like "how would the name change if I put the methyl group on carbon 2 as opposed to carbon 3?"
Stereochemistry
Assign the stereochemistry for all the stereocenters in the molecules shown below:
As you now know, stereochemistry can drastically effect the shape of a molecule and thus its biological action. See the two real-life stories below and answer some questions about when stereochemistry played a major role in the action and use of pharmaceutical drugs.
Thalidomide:
Thalidomide, shown below in two possible stereochemical arrangements, has many important therapeutic properties. However, it was used in the late fifties in a racemic mixture (mixture of both of these isomers) to treat morning sickness for pregnant people. It was later found that while R-thalidomide was responsible for the therapeutic action, the S isomer caused severe birth defects resulting in the death of ~40% of babies exposed to this drug in utero.
(a) What is the term that describes the relationship between these two isomers?
(b) Which is the therapeutic form and which is the form that caused birth defects?
Nexium:
In 2001, AstraZeneca announced that, through an improvement to the technology, the mass of the active compound in a Nexium pill (“the purple pill,” used to control acid-reflux) could be halved by using esomeprazole as shown below, instead of omeprazole. The company received backlash over false advertising. Using the structures shown below, can you spot the source of controversy?
Ethynyl estradiol is an important synthetic estrogen found in many formulations of the oral contraceptive pill. How many stereocenters are there in this molecule?
How many diastereomers does this molecule have, based on your answer?
Use this link to view the molecule in 3D. What would happen to the ring structure and overall shape of the molecule if stereochemistry wasn’t specified at each stereocenter?
Basic Reaction Chemistry
An important skill needed for determining the appropriate regiochemistry (bond formation at one atom versus other possibilities in a chemical reaction) in the products for the reactions we've seen is to be able to identify the level of substitution of a carbon atom. In the following example, label the classification of each circled carbon with labels like "primary."
Going through your notes or the online lectures, fill out the table below summarizing all the reactions we've seen. Categorizing like this helps reduce the overall cognitive load of material that might initially feel disparate, like reaction chemistry. You'll hopefully find that it's not disparate at all, and there are many connections and patterns you can realize.
The ultimate goal of organic reaction chemistry is be able to string together many synthetic steps in order to build complex molecules. Can you plan a three-step synthesis to get from the ethane reactant to the ethanal product shown below?
Saccharides
D-galactose is shown in the Fischer projection on the left below. Can you fill in the stereochemistry at each carbon to work your way to D-galactose's Haworth projection? Try this question in full and check your answer before moving onto the D-altrose example below.
This example shows the Fischer projection of D-altrose on the left below. Convert this structure to its Haworth and then chair form, using what you learned from the process and answers to the D-galactose question above.
N-Heterocycles and Aromaticity
The chart above shows many of the important heterocycles that are found as building blocks for many naturally occurring compounds as well as those made in synthetic pharmaceuticals and other lab-made compounds. They are color-coded based on the identity of their heteroatom-- as you may be noticing, blue is commonly associated with nitrogen, red is often associated with oxygen, and yellow is often associated with sulfur.
a) Identify which are aromatic.
b) Amongst the nitrogen-containing heterocycles, shown in blue, which do you expect to be easily protonated, and which are not?
Amino Acids
All amino acids are acid/base sensitive, due to the acidic carboxylic acid group and the basic amine group, and in thus in the fully protonated form, could be considered diprotic acids. Some amino acids have a side chain that also features an acidic group, making the amino acid a triprotic acid. Click here to revisit the acid/base chapter and scroll to the bottom to think about amino acids as polyprotic acids.
You may also want to review the polymer information from Chapter 12 for anything related to amino acids/peptides.
Challenge/Enrichment
Which COVID vaccine did you/will you get? You now have had enough Chemistry to speculate on the structures of most of the ingredients in the vaccines. See if you can match the ingredients from the ingredient list from the Pfizer vaccine with their structures (or, if you're a hardo, try and draw from from the list).
Some compounds may be too complicated to be able for you to correctly draw the entire molecule (even professional chemists rely on computers to convert between names and structures for very complex molecules, and some of these names are trivial names rather than systematic ones) but you may be able to correctly draw some parts of these more complicated molecules. You won't be able to draw anything more specific than a generic mRNA strand without information about the nucleotide sequence.
Pfizer Ingredient List:
mRNA, lipids ((4-hydroxybutyl)azanediyl)bis(hexane-6,1-diyl)bis(2-hexyldecanoate), 2[(polyethylene glycol)-2000]-N,N-ditetradecylacetamide, 1,2-Distearoyl-sn-glycero-3-phosphocholine, and chloesterol), potassium chloride, monobasic potassium phosphate, sodium chloride, dibasic sodium phosphate dihydrate, and sucrose.
