Tag: organic 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

{ Add a Comment }

Is it E1, E2, SN1, or SN2? [with printable chart]

Is it E1, E2, SN1, SN2??

This is such a common question, not only for students but on exams too.  How the heck do you tell the difference between an E1, E2, SN1, SN2 reaction?  Check out the chart below to start.

E1, e2, sn1, sn2


The factors that will decide:

1) Do you have a strong nucleophile?  If you do, it would favor an SN2 reaction.  If it mediocre, it will favor an SN1 reaction.

2) Does your nucleophile double as a base? If yes, it is going to favor elimination (E1/E2) over substitution (SN1/SN2).

3) How good is your leaving group?  If it is awesome, it is more likely to be a carbocation intermediate, ie E1 or SN1 reaction.  If the leaving group is only OK, that means it has to be forced off and is more likely to be a concerted reaction mechanism like SN2 or E2.

4) What is your solvent? Polar protic solvents will stabilize a carbocation better, therefore promote an E1 or SN1 reaction.  Polar aprotic solvents favor SN2 and E2.

5) What kind of substrate do you have?  If your starting material is a tertiary substrate, you are definitely E1 or SN1.  If it is a primary substrate,  you are definitely SN2 or E2. If it is a secondary substrate, it could go any one of the ways.


free organic chem study guide


Let’s look at an example.

SN1 reaction





This is an easier example, but let’s start with it.  Here is the most important thing to see: The product has OTf substituted, NOT eliminated.  Just by looking at the product, we know it has to be an SN1 or SN2 reaction NOT an E1 or E2 reaction.  Therefore, when we look at the different factors below, we are going to ignore E1 and E2.

1) Nucleophile: Cl is good but not great. Mediocre Nu = SN1

2) Basic: NaCl is not basic.  No base = SN1/SN2

3) Leaving group: OTf is a dynamite leaving group.  Awesome LG = SN1

4) Solvent: tBuOH is a polar protic solvent = SN1

5) Substrate: It’s tertiary at the leaving group = SN1

All of the factors point to an SN1 reaction, therefore I feel comfortable saying it is an SN1 reaction.


How about this one:

an SN2 reaction





This is still clearly a substitution, but it’s on a secondary substrate, so it could go either SN1 or SN2.  Here are the factors:

1) Nucleophile: CN is a great nucleophile.  Great Nu = SN2

2) Basic: NaCN is not basic.  No base = SN1/SN2, but we already knew that.

3) Leaving group: Cl is a decent leaving group. Decent LG = SN2

4) Solvent: acetone is a polar aprotic solvent = SN2

5) Substrate: It’s secondary at the leaving group = SN1 OR SN2

Almost all of the factors point to an SN2 reaction, with the notable exception of the type of substrate.  I still feel comfortable saying it is an SN1 reaction.


What do you think?  What is the most difficult substitution/elimination problem you have seen on an exam or in class?


{ Add a Comment }

Resonance between equivalent atoms in organic chemistry means equal bond lengths.

Let’s talk resonance in organic chemistry.  

Resonance in organic chemistry is one of the most fundamental and useful concepts you will learn in this class. Once most students hear this tip, it makes perfect sense to them, but it isn’t one that you might think of on your own.  Take a look at the structure below, and ask yourself: are the two N-O bonds in this molecule the same length?

resonance in organic chemistry

Since freshman chemistry, we have been told that double bonds between two atoms are shorter than a single bond between the same two atoms.  Hence, the N-O double bond should be shorter than the N-O single bond.  Spoiler: it is not.  But before we get into that, let’s look at some resonance forms of the nitro group at the end of this hydrocarbon:

resonance and bond length

Here, we can more clearly see that the nitro group is interconverting between the three resonance structures shown above.  Structure 3, where the charge is spread evenly between the two oxygens is a valid structure and shows that the bond two oxygen atoms in the molecule are equivalent and have the same bond length (124 pm).  This is shown here using the dashed bond, which you can think of as “half of a bond” for lack of a better term.


We care even more about this principle when it can be applied to more complex organic molecules where it is not obvious that the bonds are equivalent.  For example, the cyclopentadiene anion:

At first glance, this appears to have three different carbon atoms.  However, once you start looking at resonance structures, you can see that the anion can be moved to any of the carbons in the ring.  This makes them all equivalent, via resonance.  This is confirmed through analytical studies which show that all C-C bonds are approximately 137pm long.  Additionally, as this fits Huckel’s rule of 4N+2, the molecule is also aromatic.


Take Home Message: If you see symmetry or aromaticity, think equivalent bond lengths

 For more help with resonance, please see our homepage at organic chemistry



free organic chem study guide

{ Add a Comment }

Steps of a Free Radical Reaction [simplified – with a great diagram]

The steps of free radical reactions


This is one of the best depictions of the steps of free radical reactions I have seen.   It shows what can go on in this reactions and how we get from starting material to desired final product.

Steps of a free radical reaction


Initiation = 1 neutral provides two radicals.  This is what starts the entire reaction.  This is also the only initiation step that can occur, as CH4 is not going to break off an H*.

Propagation = 1 neutral + 1 radical provides a different neutral and a different radical.  In this reaction, the most likely propagation is chlorine abstracting a proton from methane to give HCl and the methyl radical.  The next step is where the methyl radical breaks up two Cl atoms.  What I really like about this depiction is that it shows that the Cl* from reaction 3 can be recycled back into step 2.  This means that the reaction is self-propagating.  This also means that IN THEORY you could have one initiation reaction, followed by a bunch of propagation, ending with one termination reaction.  Of course, in real life, for many reasons, this does not happen as there are lots of initiation reactions.

Termination = 2 radicals providing one neutral.  The part to remember here is that any two radicals can get together to terminate the reaction and form a neutral species.  Since we have 2 types of radicals in the reaction (Cl* and CH3*) , there are three combinations of potential termination steps.  Reaction 4 gives us back starting material, so it is fine.  Reaction 6 gives us product, so it is also fine.  Reaction 5 give us a byproduct, which strangely enough can replace methane in the propagation step and give us another by-product.

Think about this picture and figure out all of the side reactions that might occur to fowl up the reaction.  Then, (for you advanced students) think about what ways exist that you can minimize those side reactions.

Here is the quick summary of radical reactions:

  1. Initiation = 1 neutral provides two radicals.
  2. Propagation = 1 neutral + 1 radical provides a different neutral and a different radical.
  3. Termination = 2 radicals providing one neutral.

Hope this was helpful to you all, and as always, happy reacting.


free organic chem study guide






{ Add a Comment }

Detect Hydrogen Sulfide Using Nucleophilic Aromatic Substitution

This is some very cool chemistry.  And this post is dedicated to all of those who think that the organic chemistry you learned in your class was useless.

A professor and his graduate student at the University of Oregon have developed a hydrogen sulfide detector that can detect H2S in the parts per billion range (ppb).   This detector would be very important in the study of biologically contaminated water samples.  H2S is a colorless gas that smells like rotten eggs and is world-renown for its ability to make people sick.

This is very cool chemistry and it is performed using nucleophilic aromatic substitution.  Most of you are familiar with electrophilic aromatic substitution from second semester class, so some of you may recognize nucleophilic aromatic substitution.  Here is a quick example to refresh your memory.

In this reaction, methoxide anion is displacing fluorine in order to create the new aromatic ring.  The defining characteristic of nucleophilic aromatic substitution is that you need electron withdrawing groups on your aromatic ring to make the reaction occur.  In the above example, NO2 is our electron withdrawing group.  I am not sure what they are using in their probe (spoiler alert: i have not red the article yet), but i am sure it is something similar.

The crux of the reaction, said the study’s  graduate student Leticia A. Montoya, is the reaction process in which the probe reacts with H2S to produce a distinctly identifiable purple compound. “This method allows you look selectively at hydrogen sulfide versus any other nucleophiles or biological thiols in a system,” Montoya said. “It allows you to more easily visualize where H2S is present.”

The cite for JOC is: Leticia A. Montoya, Taylor F. Pearce, Ryan J. Hansen, Lev N. Zakharov, Michael D. Pluth. Development of Selective Colorimetric Probes for Hydrogen Sulfide Based on Nucleophilic Aromatic SubstitutionThe Journal of Organic Chemistry, 2013; :

{ Add a Comment }

Graduate School for Organic Chemistry?? Not a bad idea if I do say so myself.

Graduate School for Organic Chemistry??

A presumptuous congratulations on passing this class.  For some of you it was not easy.  For others, it might have been enjoyable.  And for a select few of you, it was so awesome that you would love to take the class again just for fun.  Right now, I am talking to that last group of students.

If you enjoyed your organic chemistry class, you might want to consider a way to continue the party. That way is to get a graduate degree in chemistry.  Here are some of the benefits to it:

1) Recruiting trips: Rent the 80’s hit movie “Johnny Be Good”.  Your recruiting trips to prospective graduate schools will not be quite that crazy, but each school you are accepted to will fly you out for the weekend to wine and dine you.  This includes meeting the faculty & current graduate students, seeing the campus, hearing about research that you might be interested in and seeing what life as a grad student would be like.  It is a great way to spend part of your senior year and is the first step to picking the perfect graduate school for you.  It is also an amazing opportunity to talk to the graduate students that are already there and find out how life at that school really is.

2) You get paid to go to school:  Almost every university that offers a graduate degree in chemistry will pay you go to school there.  No joke.  In exchange for teaching undergraduate classes and/or doing research in order to obtain your degree, these schools will pay you a stipend.  Generally, it is not much money, but it will be enough for most of you to live on.   Depending on the school, this stipend can range from $15K to $35K/year and tuition is usually covered in that (or is very cheap).  Considering that you are being paid to be a
student, this isn’t such a bad deal.

3) You get to put off starting real life:  If you get a masters degree, it will take you 18 months to three years to complete.  If you get a PhD, it will take you between 4-6 years.  This is all time in which you are still a college student and can continue to party like it is 1999.

4) You will increase your earning potential for your entire career:  With an advanced degree on your resume, you can demand higher salaries for your entire working career.

5) You don’t necessarily even need to become a chemist with your degree:  A sizable percentage of those who get advanced degrees in chemistry never actually become bench chemists, or even stay in the field of chemistry.  I know people that have become engineers, pharmaceutical sales reps, medical examiners, and even FBI agents.  The great part about it is that you have flexibility and aren’t pigeon-held into a chemistry job.

Overall, more education never hurts anyone, especially when someone else is paying for you to do it.  If you are even remotely interested in hearing more about this, I would strongly suggest learning more about a graduate degree in the sciences.  For most schools, you can visit their websites and get more information.  If you decide to start the process toward going to graduate school, you want to
take the GRE exam sometime in your junior year and start applying in the fall of your senior year

{ Add a Comment }

Organic Chemistry Help: Symmetric diols came from the Pinacol reaction

Some of your professors will try to sneak this one in on you during an exam:  Your professor will ask you to synthesize the symmetric diol shown below and you will either not know how or you will come up with a convoluted, difficult or wrong answer. 

While not obvious, there is a very simple way to create a symmetric diol using the Pinacol reaction.  Using a number of reducing agents, ketones and aldehydes can be coupled with themselves to form a symmetric diol, as shown below:


The reaction is also called the Pinacol Coupling Reaction and can be used on most aldehydes and ketones, but not on acid halides or carboxylic acids.  Now to address the original synthetic problem above:


The first step is reaction of the reaction of ethyl lithium with ethanal to form 2-butanol.  This is then oxidized to 2-butanone using Jones’ oxidation.  Now, under Pinacol Coupling conditions, 2-butanone is then reacted with itself using magnesium to form the final product. 

Take Home Message:  Symmetric 1,2 diols came from the Pinacol reaction.           


For more organic chemistry help, go to organic chemistry


Helpful Chemistry Site of the Week.

Today’s site of the week is www.chemicalforums.com.  I have been a part of this site for a while, and have been pretty impressed with it so far.  Once you register, you can post chemistry questions for the experts to answer.  The experts are extremely knowledgable, and you get a bunch of responses in a very short time.  Great resource for the undergrad who wants a quick answer to a topic that has eluded them to this point.  An even better resource for the grad student who wants to run a research idea by a 10,000 lb brainiac.

This site gets 4.5 beakers out of 5.

For further information on this, please see organic chemistry.

{ Add a Comment }

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: http://www.chemhelper.com/glossary.html


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

{ Add a Comment }