pharmacy & study organisation

Organic Chemistry: Electrophilic Additions to Alkenes

Hey all! I wanted to put together a few review guides for the reactions I learned in my organic chemistry 1 class. I’m starting off with the alkene-related reactions, specifically with electrophilic additions. Despite being super hard to fully conceptualize (I still have trouble with them!!), they’re very important to recognize, because the same patterns repeat with other reaction types, particularly with alkynes. I’ll go through each reaction type here with a quick mechanism and jot down important bits of info. But before I start, I used a lot of abbreviations, so here’s a key:

R+ is carbocation

R is any group with a carbon

IM is intermediate

X is halogen

E+ is electrophile

RDS is rate-determining step

HOMO is highest occupied molecular orbital

LUMO is lowest unoccupied molecular orbital

Squiggly lines indicate enantiomers formed due to alternating wedges and dashes

Addition of HX

Introducing Markovnikov’s rule: the formation of a more stable R+ is favored b/c it’s a lower energy process

Alkene additions proceed faster via a more stable R+ IM (kinetics)

Tri-substituted carbons are favored over mono-substituted carbons

X is added to the more substituted carbon

Always watch for stereochemistry! Enantiomers can be formed as products

Carbocation Rearrangements 

Carbocation rearrangements will occur so the R+ is as stable as possible

That’s why the Markovnikov product won’t always be the major product

Rearrangements usually occur through hydride shifts, but alkyl shifts can also happen if that’s the only possible route

Remember: always check to see where the positive charge is at− if you can shift a hydrogen or methyl group over to make that carbon extra substituted, then it’s probably right

With the orbital alignment (aka alkyl shift), there’s a filled-empty orbital overlap, where the migrating bond is aligned with the empty 2p orbital

Ring Expansions

Some questions are gonna ask you to do ring expansions, so always think alkyl shifts (again, this is so we form the most stable R+)

NUMBER. YOUR. CARBONS. This will get messy

Note that even though the di-substituted carbon doesn’t change after the first arrow, the shape changes from cyclopentane to cyclohexane, so it’s thermodynamically more stable

Hydration

This follows Markovnikov’s rule− the OH group is always on the more substituted carbon of the alkene

Also this is pretty much a repeat of HX addition, but with some acid-base action

Pro-tip: your catalyst, H3O+, is always gonna be the electrophile, and your nucleophile is always gonna be the double bond, so START THERE!

There’s gotta be water after that first step (hydration, duh)

Your water is now a nucleophile, and it’s gonna start attacking the R+

Remember to follow through with any possible R+ rearrangements− we won’t need it here b/c the R+ is already tri-substituted

Your catalyst MUST be regenerated!! *insert acid-base reaction*

Side note: alkene dehydration is the reverse of hydration and is an E1 process 

DON’T ADD H2O/H3O+ UNDER DEHYDRATION CONDITIONS

Instead, use a strong acid, like concentrated H2SO4

Oxymercuration-Demercuration

This is essentially an alkene “hydration” w/o the rearrangement part

We don’t have rearrangement b/c the mercurinium ion doesn’t have a carbon

When the mercurinium ion bridge breaks, the nucleophile (in the second example, water), attacks the MORE substituted carbon, whereas the HgOAc attacks onto the LESS substituted carbon

The OH and HgOAc add ANTI to each other, but then the H from BH4- changes orientation on the LESS substituted carbon (forming diastereomers)

Side note: as a variation, you can also use an alcohol (ROH) instead of H2O in the oxymercuration step

Hydroboration/ Oxidation

The double bond nucleophile attacks the empty orbital in BH3

The BH3 attaches onto the LESS substituted carbon, so the positive charge builds on the MORE substituted carbon

I like drawing the third H in BH3 as an extension of BH2, so I can visually see the hydride shift

The OH from the peroxide basically replaces the BH2

The specific steps with BH3 get messy, so I was taught a revised method− basically, a concerted addition of BH3 w/ an internal H- transfer

There is regioselectivity in the sense that the partial positive charge follows Markovnikov’s rule

There is stereospecificity due to the syn (same side) addition of H and BH2 in the hydroboration product

Alkene Halogenation

Note that I2 doesn’t work here as a possible halogen

Markovnikov regioselectivity is present

There is ANTI stereospecificity, as in the two individual X’s from X2 attach themselves as opposite wedges and dashes

Alkene Halohydrin Formation

This is very similar to the previous alkene halogenation, except the second X in X2 doesn’t attach onto the final product

Rather, the nucleophile replaces the second X

Markovnikov regioselectivity is also present (this is SN1-like)

There is ANTI stereospecificity yet again (this is SN2-like)

Organic Chemistry: Electrophilic Additions to Alkenes

Hey all! I wanted to put together a few review guides for the reactions I learned in my organic chemistry 1 class. I’m starting off with the alkene-related reactions, specifically with electrophilic additions. Despite being super hard to fully conceptualize (I still have trouble with them!!), they’re very important to recognize, because the same patterns repeat with other reaction types, particularly with alkynes. I’ll go through each reaction type here with a quick mechanism and jot down important bits of info. But before I start, I used a lot of abbreviations, so here’s a key:

R+ is carbocation

R is any group with a carbon

IM is intermediate

X is halogen

E+ is electrophile

RDS is rate-determining step

HOMO is highest occupied molecular orbital

LUMO is lowest unoccupied molecular orbital

Squiggly lines indicate enantiomers formed due to alternating wedges and dashes

Addition of HX

Introducing Markovnikov’s rule: the formation of a more stable R+ is favored b/c it’s a lower energy process

Alkene additions proceed faster via a more stable R+ IM (kinetics)

Tri-substituted carbons are favored over mono-substituted carbons

X is added to the more substituted carbon

Always watch for stereochemistry! Enantiomers can be formed as products

Carbocation Rearrangements 

Carbocation rearrangements will occur so the R+ is as stable as possible

That’s why the Markovnikov product won’t always be the major product

Rearrangements usually occur through hydride shifts, but alkyl shifts can also happen if that’s the only possible route

Remember: always check to see where the positive charge is at− if you can shift a hydrogen or methyl group over to make that carbon extra substituted, then it’s probably right

With the orbital alignment (aka alkyl shift), there’s a filled-empty orbital overlap, where the migrating bond is aligned with the empty 2p orbital

Ring Expansions

Some questions are gonna ask you to do ring expansions, so always think alkyl shifts (again, this is so we form the most stable R+)

NUMBER. YOUR. CARBONS. This will get messy

Note that even though the di-substituted carbon doesn’t change after the first arrow, the shape changes from cyclopentane to cyclohexane, so it’s thermodynamically more stable

Hydration

This follows Markovnikov’s rule− the OH group is always on the more substituted carbon of the alkene

Also this is pretty much a repeat of HX addition, but with some acid-base action

Pro-tip: your catalyst, H3O+, is always gonna be the electrophile, and your nucleophile is always gonna be the double bond, so START THERE!

There’s gotta be water after that first step (hydration, duh)

Your water is now a nucleophile, and it’s gonna start attacking the R+

Remember to follow through with any possible R+ rearrangements− we won’t need it here b/c the R+ is already tri-substituted

Your catalyst MUST be regenerated!! *insert acid-base reaction*

Side note: alkene dehydration is the reverse of hydration and is an E1 process 

DON’T ADD H2O/H3O+ UNDER DEHYDRATION CONDITIONS

Instead, use a strong acid, like concentrated H2SO4

Oxymercuration-Demercuration

This is essentially an alkene “hydration” w/o the rearrangement part

We don’t have rearrangement b/c the mercurinium ion doesn’t have a carbon

When the mercurinium ion bridge breaks, the nucleophile (in the second example, water), attacks the MORE substituted carbon, whereas the HgOAc attacks onto the LESS substituted carbon

The OH and HgOAc add ANTI to each other, but then the H from BH4- changes orientation on the LESS substituted carbon (forming diastereomers)

Side note: as a variation, you can also use an alcohol (ROH) instead of H2O in the oxymercuration step

Hydroboration/ Oxidation

The double bond nucleophile attacks the empty orbital in BH3

The BH3 attaches onto the LESS substituted carbon, so the positive charge builds on the MORE substituted carbon

I like drawing the third H in BH3 as an extension of BH2, so I can visually see the hydride shift

The OH from the peroxide basically replaces the BH2

The specific steps with BH3 get messy, so I was taught a revised method− basically, a concerted addition of BH3 w/ an internal H- transfer

There is regioselectivity in the sense that the partial positive charge follows Markovnikov’s rule

There is stereospecificity due to the syn (same side) addition of H and BH2 in the hydroboration product

Alkene Halogenation

Note that I2 doesn’t work here as a possible halogen

Markovnikov regioselectivity is present

There is ANTI stereospecificity, as in the two individual X’s from X2 attach themselves as opposite wedges and dashes

Alkene Halohydrin Formation

This is very similar to the previous alkene halogenation, except the second X in X2 doesn’t attach onto the final product

Rather, the nucleophile replaces the second X

Markovnikov regioselectivity is also present (this is SN1-like)

There is ANTI stereospecificity yet again (this is SN2-like)

Hey guys, so just as a heads up, I don’t think that highlighting your already made notes is that effective unless it’s for aesthetic. However for many subjects like English classes or humanities, you are often given a bulk amount of readings and I believe that highlighting not only helps you digest the content but it also makes note taking easier afterwards. Though some people find it hard to figure out what they need to be highlighting so I’ve come up with a few ideas.

Terms often come into play when digesting a lot of textbook readings where ideas are being explained to you and often you will want this definition to be readily available when revising too so its good to highlight these when you come across them.

Key concepts can be really good to highlight when trying to understand scientific concepts within research articles or when reading persuasive texts as you can relate the material back to your core unit of work. Alternatively you can use concept to highlight the main idea of paragraphs or chapters to give you a quick reference of summary when studying.

I find examples to come particularly handy in studies which are applied to everyday situations, for example a law textbook may discuss a concept and give an applicable example which I would then highlight. Or in math you may highlight an example problem to help you if you get stuck later.

This highlighter was a godsend in my last exams, especially for history because I’d be reading so many historians and articles and when it came to writing essays it would only take me seconds to find a good reinforcing quote as I’d been highlighting them all along. Or even in English you can highlight quotes from reviews or scholars to be used to back up your argument.

This one is mainly for English and literature studies because when analysing devices and giving examples of these it helps when they are already highlighted. It’s all about studying smarter not harder and getting things done efficiently so this step really has helped me out.

Again another more humanities point as you often have to create a mental catalogue of people involved and the context of situations to understand the severity of moments in history. Though in science and other subjects it’s always good to know what pages are talking about what professors or scholars or historical figures.

Finally, in many subjects you are expected to produce a mental timeline of events especially in history and it becomes confusing to pinpoint events and dates together so this step helps to take the labour out of that situation.

Here’s How:

To decide which reactant is in excess (more than required for the reaction) and which is the limiting reactant (not in excess) you need to know two things: the mole ratio of the reactants and the number of moles of each reactant.

Mole Ratio:

The mole ratio of the reactants can be taken from the balanced equation i.e.

It is important to note that the equation must be balanced (have the same number of atoms of each reactant on each side).

In the above equation, the mole ratio of Magnesium to Hydrochloric Acid is 1 : 2.

Number of Moles of Each Reactant:

If you are not given them, you can work out the number of moles of each reactant using these formulae:

where:

n = number of moles

C =  concentration

V = volume

m = mass

gfm = gram formula mass

Deciding Which Is In Excess/Limiting:

It is then relatively simple to work out which reactant is in excess.

Pick one reactant and place that into the mole ratio as shown, then work out how many moles of the other reactant would be needed for this reaction. If the amount of moles needed is less than the amount of moles given of this reactant, then it is in excess. If the amount of moles needed is greater than the amount of moles given then it is limiting.

(for this example assume the number of moles worked out for Magnesium is 2 and the number of moles worked out for Hydrochloric acid was 5)

Now you know that Hydrochloric Acid is in excess and thus Magnesium is the limiting reactant.

Taking it further:

After finding out which reactant limits the reaction, you may be asked to decide how much of a product is produced. This is pretty simple. You only need to know the mole ratio of the limiting reactant to the product and then you can work as above.

(for this example assume we were asked to find how much hydrogen was produced)

The mole ratio here is 1 : 1

So, two moles of Magnesium would give you two moles of Hydrogen.

(Using given Gram Formula Mass)

1 mol of Mg = 24.3g = > 2 mol of Mg = 48.6g

1 mol of H2 = 2g = > 2 mol of H2 = 4g

Thus, 4g of Hydrogen was produced.

Also See:

My IUPAC Nomenclature for Organic Chemistry Masterpost for High School Chemists

online resources

chemistry exams

sparksnote chemistry study guide

crash course chemistry videos

concept tests

thattutorguy’s chemistry videos

studystack’s chemistry flashcards

printable periodic tables

tips for studying chemistry

general chemistry glossary

chemistry revision

another chemistry revision website

chemistry lecture notes

dynamic periodic table

writing chemistry notes

faces of chemistry

chemistry timeline

creating chemistry flashcards

website that balances your chemistry equations

inspiration

mind maps

chemistry notes

more chemistry notes

periodic table graphic

How Do Medicines Work?

When you’re looking at two compounds and wondering how they may react, pay attention to the carbons - if they are bonded to a halogen or something more electronegative than them, then they have a partial positive charge and they’re going to want anything that will give them more electrons (a.k.a. a nucleophillic attack). If they’re bonded to hydrogen, they have a partial negative charge and they become your nucleophile, which will want to give those electrons to something that’s lacking them. Once you get these basics down, mechanisms become much easier to memorize because you can see the logic in them and sometimes predict them.

Get the basic mechanisms ingrained in your brain. Think of SN1, SN2, E1 and E2 as your new multiplication table. Make flashcards about them and take them to class. Or put them at the back or front of your notebook. Just have them handy at all times.

Draw the final steps in 3D. ALWAYS. You can draw the mechanisms and the first steps in 2D because it will make it easier to understand, but never forget that you’re working with a 3D structure that can flipped (and attacked by nucleophiles) every which way. Also, if you don’t know the basic perspectives used in orgo (Fischer, Newmans, sawhorse, wedge-dash) please take half an hour to learn them. Mainly wedge-dash and Fischer, but Newman is very useful when deciding which position you should put your atoms in if you’re dealing with sin and anti.

Colors. If you’re one of those people who ONLY writes in black pen, awesome, keep using it for WRITING. For reactions though, you’re going to want options. you’ll need to differentiate between:

The molecules (same color for atoms and bonds, unless you want to finish your notes on your deathbed).

Your three types of arrows: electron flow, actual steps in the reaction (think intermediates) and steps you may take to make it clearer for you but that happen at the same time.

Formal charges

The electrons that stay with its original atom and the ones that are given/shared, if you’re like me and you like your mechanisms to be spelled out.

This is not an excuse to go nuts with the coloring, 3 colors are enough. Personally, I use purple for molecules, electrons and reaction arrows, black for electron flow arrows and charges and light blue for clarification step arrows. Also optional but to denote a homolytic fission I usually write a blue line perpendicular to the bond. Similarly, if two atoms share one electron each, instead of just one them donating both electrons, I link said electrons with blue.

Remember to be consistent, otherwise you’ll end up like me, looking at your notes from the beginning of the semester and wondering if that dash is a bond or a -1 formal charge (to avoid this, preferably circle formal charges. Lol I never do this but I should).

Flashcards are so helpful! Write the reactants on one side and the mecanism and products on the other. Test yourself until you are one with the electrons.

If it’s a concerted mechanism, number the arrows. You’ll thank yourself a month from now.

Khanacademy. Khanacademy will save your butt when it comes to mechanisms. Chemwiki is likely to have anything that Khanacademy doesn’t. If it isn’t in either of those, Google images just became your new best friend. Books also tend to explain those nicely but I personally find them to be poorly structured and they usually include much more info than what you’ll actually be requiered to know. If you have the time to read two pages on a reaction though, by all means go for it.

Study in advance. Good luck studying for your final two days before if you don’t understand the mechanisms and you don’t have your material organized. Seriously, don’t do it. A week before the exam you could make those flashcards mentioned above. They’re a great way to review but it will be impossible if you are learning these things from scratch.

Get your hands on past tests. This goes for any subject but especially for orgo. Try to get a past test or at least ask an upper-classman who’s taken orgo with that professor. Does his/her tests focus on mechanisms? Retrosynthesis? Or does he/she give you the reactants and ask what the product is or what environment they should be in to obtain x? Ideally, you should be able to answer any of these if you know the material. However, if they focus on retrosynthesis, it may be a little tricky, so make sure to cater your study techniques to that.

You should also check out @colllegeruled’s Surviving Organic Chemistry, it’s super helpful and it has lots of resources (seriously, you introduced me to Khanacademy, I OWE YOU MY LIFE).

So, this is what I can offer so far. I hope it shines at least a faint light into the dark path that is organic chemistry.

Other masterposts

How To Stop Procrastinating

Memorization Tips

Skincare 101

notes masterpost

Hi! OMG IM FINALLY DONE POSTING ALL MY NOTES HAHAH FINALLLYYYY!!!!

I understand it’s pretty hard to collate all my notes together, so I’ve made this masterpost!! :) + some abbreviation legend thing just in case you guys don’t understand the abbreviations i wrote hehe i hope you guys enjoyed these and that these notes helped!! thank you for sticking by me and my irregular posting schedules. Will continue to update this list when i post more notes in the future !!! xx

Biology Notes - based on Biology Matters for GCE ‘O’ Level (2nd Edition), by Marshall Cavendish

Chapter 2 - Cells

Chapter 3 - Movement of Substances

Chapter 4 - Nutrients

Chapter 5 - Enzymes

Chapter 6 - Nutrition in Humans

Chapter 7 - Nutrition in Plants

Chapter 8 - Transport in Humans

Chapter 9 - Transport in Plants

Chapter 10 - Respiration v1, v2

Chapter 11 - Excretion

Chapter 12 - Homeostasis

Chapter 13 - Nervous System

Chapter 14 - The Human Eye

Chapter 15 - Hormones

Chapter 16 - Cell Division v1, v2

Chapter 17 - Reproduction in Plants

Chapter 18 - Reproduction in Humans v1, v2 

Chapter 19 - Heredity

Chapter 20 - Molecular Genetics

Chapter 21 - Ecology

Chapter 22 - Our Impact on the Ecosystem

Chemistry Notes - based on Chemistry Matters for GCE ‘O’ Level (2nd Edition), by Marshall Cavendish

Chapter 1-7

Chapter 8-14

Chapter 15-20

Study when sleepy.

Bedtime stories are for wimps. Instead of reading The Berenstein Bears, try studying for a few minutes right before hitting the hay. During sleep, the brain strengthens new memories, so there’s a good chance we’ll remember whatever we review right before dozing off . (Just try not to bring work into the actual bed, since it can make it harder to get a good night’s sleep.) And though bedtime is primo study time, it might also help to crack open the books after cracking open those eyes in the A.M.—in the morning, the brain still has lots of room to absorb new information.

Space it out.

A relatively new learning technique called “spaced repetition” involves breaking up information into small chunks and reviewing them consistently over a long period of time. So don’t try to memorize the entire periodic table in one sitting—instead, learn a few rows every day and review each lesson before starting anything new.

Tell a tale.

Turning the details you need to remember into a crazy story helps make the information more meaningful. For example, remember the order of mathematic operations PEMDAS this way: Philip (P) wanted to eat (E) his friend Mary (M) but he died (D) from arsenic (AS) poisoning.

Move your butt.

Research suggests studying the same stuff in a different place every day makes us less likely to forget that information. That’s because, every time we move around (from the library to the coffee shop, or the coffee shop to the toilet seat), we force the brain to form new associations with the same material so it becomes a stronger memory.

Switch it up.

Don’t stick to one topic; instead, study a bunch of different material in one sitting. This technique helps prepare us to use the right strategy for finding the solution to a problem. For example, doing a bunch of division problems in a row means every time we approach a problem, we know it’ll require some division. But doing a series of problems that require multiplication, division, or addition means we have to stop and think about which strategy is best.

Put yourself to the test.

Quizzing ourselves may be one of the best ways to prepare for the real deal. And don’t worry about breaking a sweat while trying to remember the name of the 37th U.S. president (fyi, it’s Nixon): The harder it is to remember a piece of information in practice mode, the more likely we are to remember it in the future.

Write it out.

Put those third-grade penmanship lessons to good use. Research suggests we store information more securely when we write it out by hand than when we type it. Start by recopying the most important notes from the semester onto a new sheet of paper.

Make me wanna shout.

Reading information out loud means mentally storing it in two ways: seeing it and hearing it  . We just can’t guarantee you won’t get thrown out of the library.

Come together (right now).

Group work doesn’t fly with everyone, but for those who benefit from a little team effort, a study group’s the way to go. Pick a few studious pals and get together every few days to review the material. Put one person in charge of delegating tasks (snack duty, music selection) and keeping the group on target with its goals.

Treat yo’ self!

A healthy holiday cookie, a walk around the block, five minutes of tweet-time: whatever floats your boat. Knowing there’s a little reward waiting for us at the end of just a few pages makes it easier to beat procrastination while slogging through a semester’s worth of notes.

Drink up.

Sorry, not that kind of drink. Instead, hit the local coffee shop for something caffeine-filled; there’s lots of research suggesting coffee (and tea) keeps us alert, especially when nothing seems more exciting than the shiny gum wrapper on the library floor.

Take a time out.

Taking time to plan is one of the most important skills a student can have. Don’t just start the week with the vague goal of studying for a history exam—instead, break up that goal into smaller tasks. Pencil it in on the calendar like a regular class: For example, allot every day from 1 to 3 p.m. to review 50 years’ worth of info.

Gimme a break.

The KitKat guys said it, and so does science: Taking regular breaks can boost productivity and improve our ability to focus on a single task  . For a real productivity boost, step away from the screen and break a sweat during a midday gym sesh.

Work it out.

Get stronger and brainier at the same time. Research has found just half an hour of aerobic exercise can improve our brain-processing speed and other important cognitive abilities. Jog a few laps around the block and see if you don’t come back with a few more IQ points.

Daaaance to the music.

As anyone who’s ever relied on Rihanna to make it through an all-night study session knows, music can help beat stress. And while everyone’s got a different tune preference, classical music in particular has been shown to reduce anxiety and tension. So give those biology notes a soundtrack and feel at least some of the stress slide away.

Nix the ’net.

We’ve all been there, facing the siren call of a friend’s Facebook wall on the eve of a giant exam. If a computer’s necessary for studying, try an app (such as this one) that blocks the Internet for a short period of time and see how much more you get done.

Say om.

Just before staring at a piece of paper for three hours, stare at a wall for three minutes. Research suggests meditation can reduce anxiety and boost attention span. While those studies focus mostly on regular meditation, there’s no harm in trying it out for a few minutes to calm pre-test jitters.

Doze off.

When there’s a textbook full of equations to memorize, it can be tempting to stay up all night committing them to memory (or trying to). But all-nighters rarely lead to an automatic A—in fact, they’ve been linked to impaired cognitive performance and greater sensitivity to stress  . In the days leading up to a big exam, aim to get those seven to nine hours a night so sleep deprivation doesn’t undo all the hard work you’ve put in.

Own the Omegas.

Omega-3 fatty acids, found in certain fish, nuts, and olive oil, are known for their brain-boosting potential. One study found that eating a combination of Omega-3-and Omega-6 fatty acids before an exam actually reduced test anxiety.

Omega-3 fatty acids, found in certain fish, nuts, and olive oil, are known for their brain-boosting potential. One study found that eating a combination of Omega-3-and Omega-6 fatty acids before an exam actually reduced test anxiety  .

Feel free to inhale.

Dusty old library again… or spa day? Research has found that catching a whiff of essential oils (like rosemary or lavender) can help calm students down before a big exam  . Skip the frantic last-minute review and try a few minutes of aromatherapy instead.

Practice your brain pose.

Hardcore yogis tend to have better cognitive abilities—especially attention span—than folks less familiar with Down Dog  . A few daily sun salutations may be all it takes to keep centered during finals period.

Learn what works.

Some people are early birds; some are night owls; some prefer to study with a pal; others need complete and total silence. Experiment to find what’s most effective for you, and then stick with it!

When you realize that you’ve only got two weeks of rotations left… and then barely enough time to study for major exams… and then before you know it you’ll be graduating from med school… 😱 #wheredidthetimego