Browsing: o-chem help

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

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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






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Functional Groups in Organic Chemistry [with diagrams]

Functional Groups in Organic Chemistry

Welcome back.  Let’s not beat around the bush on this one: functional groups in organic chemistry are why we can do any organic chemistry in the first place. Functional groups are the basis of why molecules can and will react with each other. Without functional groups, everything would be straight chain alkanes and other boring hydrocarbons. So it’s important to learn functional groups, and how they will interact with nucleophiles and electrophiles to react to form new organic molecules.

Major Disclaimer:  This is not meant to be a comprehensive review of all of the functional groups out there, however it’ll be a nice start and a good reference for you.

Hopefully you understand why they are important, now we just have to determine what some of the different types are.


functional groups in organic chemistry

What to learn about nucleophiles?  Click on the link to check it out



Hydrocarbons: these are simply composed of carbon and hydrogen. This group is alkanes, cycloalkanes, alkenes, and alkynes.  Don’t forget about conjugated alkenes too, as they are important in many organic processes such as the Diels-Alder reaction.  While alkanes and cycloalkanes are not particularly reactive, alkenes and alkynes definitely are.

Carbonyls: a “carbon double bond oxygen” is a carbonyl.  It is one of the more important electrophiles you will see in this course.  While there are different variations which can make the carbonyl more or less reactive, the basic functional group is still the same.  The important point here is to know which types of carbonyls are more electrophilic and which ones are less. Generally speaking, if there is an electron withdrawing group attached to the carbonyl carbon, that carbonyl will be more electrophilic and more reactive.

Alkyl Halides: alkanes which are connected to a halogen atom (F, Cl, I, and Br) are good electrophiles.  These can participate in nucleophilic substitution reactions and elimination reactions.  They reactivity depends on the type of alkyl halide (F, Cl, I, Br), its substitution (primary, secondary, tertiary) and the desired reaction (SN1, SN2, E1, E2).

Alcohols, Amines, and Thiols: these are generally very good nucleophiles, as the heteroatoms have lone pairs which will attack an electrophile.

Ethers: do not undergo many organic reactions themselves, but sometimes can be the product of a reaction.  Some chemists refer to ethers as “dead molecules” because of their low reactivity.



And now for some crazy functional groups….







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How to study for organic chemistry?

How to study for organic chemistry?


How to study for organic chemistry? I get asked this question pretty frequently…and while there is no easy answer (because every student is different), here is the four-pronged solution that we have come up with here.  This answer is based on a survey of organic chemistry professors that we conducted a while back.  They told us the best ways to study and the ways to avoid.  If you are interested in looking at the results of the entire survey, you can find them here—> how to pass organic chemistry (or even get an A).  We will summarize it for you here though.  It is actually pretty simple.

Situation: the organic chemistry is coming soon.  Too soon!  Not nearly enough studying has been done yet.

Step 1: Watch some organic chemistry review videos. It is really helpful to hear someone else teach the material in a little bit different way, and review videos will condense the material down for you. Here are our favorites organic chemistry videos (which happen to be ours)

Step 2: Work practice tests and practice problems. Over 90% of the professors we surveyed said this was the best way to learn organic chemistry. There are organic chemistry test banks out there (see organic chemistry test bank) that will work wonders for you.

Step 3: Find some good flashcards and practice non-stop with those. If you can’t find decent ones, make your own and emphasize the topics you didn’t do well with in step 2.  Good old fashioned 3’x5′ index cards work great.  Making them will help you learn the material even better.

Step 4: If you can, learn the material rather than memorizing it.  Organic chemistry is a discipline that requiring understanding…HOWEVER if you are pressed for time, then just memorize the heck out of it now and then go back and LEARN it before the final exam.

Hope this was helpful.  Obviously learning a complex subject like organic chemistry is more difficult than just four easy steps, but if you study hard it will go just fine.


free organic chem study guide

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86 Tricks To Ace Organic Chemistry – Multimedia Edition is now available for the iPad is very proud to announce the release of it’s best-selling book, 86 Tricks To Ace Organic Chemistry, as an iPad multimedia book. In addition to the material that made the previous version a must-read, it now also contains videos, flash cards and practice problems, making it an instant hit. It is quite a wonder and a must see on the iPad.

Now available in the iBookstore for only $7.99, it really is something to see.

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Electrophilic Addition and Electrophiles: What makes a good electrophile?


Electrophilic Addition

Electrophilic addition–Just like in football, it is easy to say that one of the players is the most important one in the game.  While many (nerdy) organic chemists could have a robust debate over a pint as to which of the compound class is most valuable in the reaction, we are going to treat them all as important.  In its most basic form, they are all essential in some way or another to the reaction’s success.  Hence, we are going to start with acids and discuss all of the compound classes one by one.

Electrophiles are one of the two most important reactants in organic chemistry.  As we have discussed previously on this blog, organic chemistry reactions are all about the flow of electrons, and electrophiles are the ones who want those electrons. When you think of the word “electrophile” you should think of the Greek word “Philos” which means “to love”.  Therefore, an electrophilic species is one that loves electrons.  Easy enough, right?   Since opposites attract, and the electrophile loves electrons, then it must be that the electrophile is positively charged. Most often, you will see this abbreviated as “E+”.

So the question now becomes: what make an atom a good electrophile and how do we spot it? Since we know the electrophiles want to electrons, the first clue that something is electrophilic is that it has a positive charge. The second clue is if we can place a positive charge somewhere on the atom via resonance and that it has an empty orbital (positive charge or metal with an empty orbital) or can get an empty orbital by kicking off a leaving group.  Below are some common classes of electrophiles you will see frequently in your course:


In example A, a carbonyl is shown. We know that the carbon of the carbonyl is electrophilic because we can place a positive charge on it via resonance. This means that a nucleophile will attack the carbonyl at this carbon atom.  In example B, we show diatomic chlorine. Diatomic halogen molecules are electrophilic because the bond between the halogen atoms as polarizable, meaning that the electrons can reside on either atom at any time, making one of the atoms more electrophilic than the other.  In example C, we see that alkyl halides are also electrophilic because of a polarizable bond between the carbon and the chlorine atoms.  Unlike example B, example C is a permanent dipole.  Example D is an example of a strong acid completely disassociating, which gives off a proton as the electrophilic species. Finally in example E, we see it you can create an electrophile from a non-electrophilic molecule. Here we have reacted nitric acid with sulfuric acid to form the nitronium ion, which is highly electrophilic.


free organic chem study guide


Take home points on electrophiles:

1)      They want electrons, meaning they are electron deficient.

2)      They are attacked by nucleophiles.

3)      They are positively charged, polar and/or polarizable.

4)      They become better electrophiles in the presence of Lewis acids.

Would you like to learn about the nucleophiles that will attack these electrophiles?  Please go to strong nucleophiles to get a good flavor of those.


And now, electrophilic addition reactions:






For more help with organic chemistry, please see organic chemistry help





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Organic chemistry help: free iPhone app

Hey everybody. So there is a free organic chemistry app for the iPod/iPhone in the iTunes app store. It is called “Organic Chemistry Essentials” and it rocks. There are over 15 different sections to help with organic 1 and 2 classes and even has a section of nerd humor.

As of today, it was downloaded over 40,000 times and has a 4.5 star rating. We highly recommend this. Give a try, it is free so you have nothing to lose.

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Organic Chemistry Help: “Eject! Eject! Eject!” Carbonyls with an ejectable group are added to twice.

These functional groups remind me of 1985 when Maverick flew through the jet wash and Goose and he had to eject from their F-14 Tomcat.  What does this title mean?  What we are trying to say is that carbonyls can be classified two different ways: ejectable or non-ejectable.  What this means is that sometime when a carbonyl is attacked by a nucleophile the carbonyl will eject one of its substituents before it reduces the carbonyl to an alcohol.  After the group has been ejected, then a second equivalent of nucleophile will reduce the carbonyl to alcohol.

In essence, this means if a carbonyl has an ejectable group on it, a nucleophile will add twice to that carbonyl.  Some examples of ejectable and non-ejectable systems are below:

In terms of synthesis, we will then observe the following:

As shown above with the ketone and the aldehyde (which have non-ejectable substituents), the Grignard reagent can only add once to the carbonyl, giving an alcohol as the product in both instances.  However, in the case of the acid halide and ester (which have ejectable groups attached) the first equivalent of Grignard kicks off the ejectable group to give a ketone.  This ketone can then be reacted with another equivalent of Grignard reagent to give the final product, which is a tertiary alcohol.   In the example above, we have added two equivalents of Grignard to the starting material in two different steps.  However, if the alcohol is your desired end-product, you can do this all in one step by adding two or more equivalents of Grignard reagent.

Take Home Message: Nucleophiles will substitute twice at the carbonyl if the starting material is an acid halide or an ester.

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Free Organic Chemistry App for iPhone/iPod Touch

Hi everybody, so has teamed up with an iPod developer and has released an app to give a little on-the-go aide in organic chemistry.  The app is called “Organic Chemistry Essentials”, the rating so far is 4.5/5 stars from users, and is free. 

It has 10-15 sections and gives tricks and tips to nail organic chemistry.  It is a great app, and best of all it is free.  I strongly recommend it.    Link is organic chemistry app

Here is one review on it: “Simply laid out, but it is very helpful, and the humor (both within the lesson and on its own) provide compic relief along with helping the reader to remember.  Very fun”

As always, for help with all of organic chemistry, please go to organic chemistry

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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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