Browsing: chemistry

Know the “normal” state for common organic atoms [3 rules to live by]


Structures of molecules can be difficult to piece together at first when you are just starting in an organic chemistry class. Hopefully you retained some of this knowledge from general chemistry. If not, one of the tricks that can greatly help with this is to know the uncharged or “normal” state for atoms that are commonly found in organic molecules.   Here is a table of the most common of those:

      – C has four bonds and no lone pairs

       – N has three bonds and one lone pair

       – Halogens (F, Cl, Br, I) have one bond and three lone pairs. 

       – O has two bonds and two lone pairs

       – H has one bond and no lone pairs


Three more rules:

–          C, N, O are central atoms, meaning that they will always be in the middle of your molecule.

–          H and halogens are terminal atoms, meaning that they will only have one bond and be at the ends of molecules.

–          With the exception of H, atoms in group I & group II are only counterions (+1 or +2 and not involved in resonance).


Remember, these rules are for when the atom is uncharged; this does not apply to charged atoms.  For example, a carbocation (a positively charged carbon atom) will have only three bonds with no lone pairs while a carbanion (a negatively charged carbon atom) wlll have three bonds with one lone pair, and a carbene will have two bonds with two lone pairs.

Notice that all of these carbons still follow the octet rule.  However, beware of atoms that do not follow the octet rule, as phosphorus is an example of an atom that can have more than an octet of electrons.  Shown below is triphenylphosphine oxide, a byproduct of the Wittig reaction.

Elements with open d-subshells, like phosphorous and sulfur, do not always follow the octet rule.  More examples of this are SF6 and PCl5.  However, carbon, nitrogen and oxygen will follow the octet rule.


free organic chem study guide

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Organic Chemistry Help: Fischer Projections are a Black Tie Affair

Emil Fischer is considered by many to be the greatest organic chemist to ever live.  His problem was that he created a way of looking at organic molecules that is very confusing to undergraduates.  These structures are necessary to learn and are very helpful when looking at certain molecules (such as carbohydrates), but they are also very easy to jumble.  This is because Fischer structures are drawn as crosses, which could lead one to erroneously think that the central carbon is flat, when it is actually still tetrahedral.

The easiest way to look at these is to think of them as bowties that have been strung together:

3-dimensionally speaking, the substituents that are on the sides of the structure are depicted at the end of the bowtie and are represented as “coming out of the paper”.  The backbone is composed of dashed lines, which are meant to represent that those portions “are going into the paper”.  This is now a much easier way to view these structures, as it is more apparent what area each substituent occupies.

The useful part of the bowtie projection is that it is now easier to assess the stereochemistry at each chiral center.   It should be much easier to visualize that the bottom chiral center is “R”.  This was not as obvious when viewing the Fischer projection as a cross

For more help like this, please go to organic chemistry

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The Good, The Bad and The Ugly of Summer Organic chemistry classes

Congrats on getting done with your finals!  Not an easy task sometimes.  But on the topic of today’s post, I was recently asked what I thought about students taking o-chem classes over the summer.  This is not an easy “yes or no” question, and definitely depends on the student.  Here are some of the considerations:

The Good:

1. It is only usually 5 weeks long. 

2. If you are not working this summer, it is much better than just sitting around doing nothing.

3. If you are not majoring in chemistry and don’t want to go to med school, it is a great way to get it out of the way quickly.

 The Bad:

1. If you ARE majoring in chem, it is very easy to forget everything that you learned in the class because you crammed it all into 5 weeks.

2. Classes are usually at least 3 hours per day, plus homework every night and an exam once a week.  This can be overwhelming.

The Ugly:

1. If you get a bad prof, keep the hemlock close.

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You can actually see molecules!?!

Hi everybody, we are back from the long summer break and I wanted to start the year with a very cool article which just came out.  They have taken a molecule of pentacene and provided a “clear as day” picture of it.  It is pretty fascinating to look at the ring structure and see how similar it is to the molecular models we have all been using since freshman chem.  Anywho, link is below, well worth a quick peek:

Remember, all your needs for organic chemistry can be found at organic chemistry


Good luck, and as always, happy reacting.

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Learning Organic Chemistry is Like Learning Another Language

Learning organic chemistry is like trying to work in a foreign country where if you don’t know the language, it is going to be very difficult to learn how to do your job.  You have just been transported to the mythical country of “ochemia”, a small island nation in the south Pacific, where your job is to write chemistry reactions. 

Frequently, in a chemistry lecture, professors start tossing out organic chemistry terms far too quickly.  Because students aren’t fluent in “ochemia” yet, they need to translate each word in their head to understand what the instructor has just said.  By the time this mentally translation is done, the student has just missed the next sentence and has lost half of the lecture.  Our goal is to get as fluent as we can in the language of chemistry as quickly as we can.  Here are some terms it will be helpful to memorize so that you don’t have to do a mental translation when you hear them:

Meth = 1

Eth= 2

Prop = 3

But = 4

Pent = 5

Hex = 6

 Hept = 7

Oct = 8

Non = 9

Dec = 10

Electrophile = wants electrons, has a positive or partial positive charge

Nucleophile = has electrons, has a negative or partial negative charge

Halogen = F, Cl, Br, I

Aprotic solvents = do not contain OH or NH bonds

Protic solvents = contain OH or NH bonds

Lewis Acid = electron acceptor

Lewis Base = electron donor

Carbonyl group =  (C=O)

Cis = same side of a double bond or ring

Trans = opposite sides of a double bond or ring



A comprehensive organic chemistry glossary can be found at:


As always, for more help in organic chemistry, please go to Organic Chemistry

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Organic Chemistry Study Tips: Study In Packs

This reminds me of my favorite video on YouTube (  You are a pack of wildebeest, just chilling out by the water, trying to score a good grade in organic chemistry.  But you are being hunted by pride of hungry lions (your professors) who would like nothing better to make a quick snack of the weakest one of you.   After crouching in the brush, they suddenly pounce (pop quiz) and grab a hold of the smallest one of you (the student with the hardest course load). 


Two things can happen at this point:  Either the rest of the pack of wildebeest will cut their losses and try to save themselves or they can go back and heroically battle the lions to save their fallen colleague.  I am not going to ruin the video if you have not already viewed it, but I think you already know what happens. 


Studying in packs presents a number of benefits other than just altruistically helping a lesser student:

1)      Studies have shown over and over that studying in groups directly leads to higher grades of all involved.

2)      Studying in groups is generally more enjoyable for people, which leads to more time spent on the subject.

3)      If you are weaker in one area of the course, you have the opportunity to have a peer explain it to you.  Many students are more likely to understand a peer’s explanation over a stuffy professor’s.

4)      If you are stronger in one area of the course, you will strengthen your overall understanding of chemistry by teaching it to someone else.


Of course, when you are choosing study partners on the Serengeti, you need to be very careful to stay away from the jackals.  These are the students that are more parasite than human and will just leach off of your talents.  They are more succubus than man and will not help you much.   We suggest finding study partners that are interested in a good grade and are willing to put in the time necessary to achieve a good grade in the course.      

For more information and organic chemistry help, please go to organic chemistry

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Organic Chemistry Help: Resonance

Hi Everybody–Resonance is one of those issues that you will have to deal with for both semester I & II organic chemistry.  It is much better to have a solid understanding of it now, rather than have to worry about it later.  The basic goal of resonance structures is to show that molecules can move electrons and charges onto different atoms on the molecule.  This makes the molecule generally more stable because the charge is now delocalized and not “forced” on an atom that does not want it.


Below are some handy rules of resonance.  If you learn these and think about them when tackling different resonance problems, you will be able to handle whatever is thrown at you.


1) Know each atom’s “natural state”.  You need to recognize what each atom generally looks like, in an uncharged state.  This will help you to construct the Lewis Dot structure on which you will base your resonance structures.  In most uncharged cases:

       – C has four bonds and no lone pairs

       – N has three bonds and one lone pair

       – Halogens (F, Cl, Br, I) have one bond and three lone pairs. 

       – O has two bonds and two lone pairs

       – H has one bond and no lone pairs

       – With the exception of H, everyone in group I & group II are only counterions (+1 or +2 and not involved in resonance).

Remember that halogens and hydrogens are always terminal, meaning that are at the end of the molecule and only have one bond, and therefore, they will not participate in resonance.

2) Atom positions will not change.  Once you have determined that an atom is bonded to another atom, that will not change in a resonance structure.  If they do change, it is no longer a resonance strucutre, but is now a constitutional isomer.


3) Check the structure you have created to make sure that it follows the octet rule.  This will become much easier once you have a better handle on the “natural state” of atoms.


4) When two or more resonance structures can be drawn, the one with the fewest total charges is the most stable.  In the example below, A is more stable than B.



5) When two or more resonance structures can be drawn, the more stable has the negative charge on the more electronegative atom.  In the example below, A is more stable than B.


6) In the end, each resonance structure should have the same overall charge and total number of electrons (bonds + lone pairs) as when you started.


Organic Chemistry Help: More on Electrophilic Aromatic Substitution

Hey Everybody, here is a good trick to keep in your back pocket if you run across an EAS question where you have something in the ortho position, but not the para.

Here is a good trick to do it: First, bromonate your benzene ring under standard condition, then sulfonate using SO3/H2SO4.  This will make the para bromo sulfonate.  Now the next substituent, our chlorine, will be directed ortho to the bromine.  We now have a trisubstituted arene ring and can remove the sulfonate unsing acidic water.  This gives us a nice route to the ortho di-halide without having to justify why we got a mixture of the ortho and para products. 


For more information on this, please go to organic chemistry

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Organic Chemistry Help: Resonance and SN1/SN2

Hi everybody, I wanted to talk briefly today about resonance and sterics and how it can affect and SN1 or SN2.  For background, I hope everyone knows when it comes to SN1 reactions, tertiary substrates are the fastest and primary substrates are the slowest (because of carbocation stability).  Conversely, when it comes to SN2, it is all about steric hindrance, so primary is the fastest and tertiary is the slowest.  But what happens when there are other factors involved?

As shown here, the benzyl cation was a primary cation, but can undergo resonance stabilization that moves the cation all throughout the ring.  This serves to further stabilize it and makes the benzyl cation have the reactivity of a secondary carbocation when it comes to SN1.

Lesser known is the neopentyl bromide, which is a primary substrate so it should react quickly via SN2, but it does not.  This is because, even though it is primary, it has a very large t-butyl group close, which blocks the reaction site.  This makes neopentyl bromide less reactive than one would expect.  In fact, it has reactivity somewhere between a secondary and tertiary substrate, for SN2 reactions.

For more information on this, please visit Organic Chemistry.


As always, good luck and happy reacting.

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