Tag: organic chemistry help

Organic Chemistry rules: Always, sometime, never.

Organic Chemistry Rules: Never violate these!!

Disclaimer:  This posting applies to Undergraduate organic chemistry.  This does NOT apply to crazy physicists who create all sorts of insanity in a laboratory that cannot exist outside a xenon forcefield.

In organic chemistry, like in life itself, there are rules.  Some of them (known as the “always/never” rules) should never be violated, such as always wash your hands leaving the bathroom, or never spit in church.  Other rules (known as the “sometimes” rules) are guides that you should be aware of rather than hard rules. 

Thus, we present a blog post called “Organic Chemistry Rules: ALWAYS, Sometimes, NEVER.”


1) Hydrogen ALWAYS has only one bond to it.  You will never see an organic molecule that has two bonds to hydrogen.

2) Carbon NEVER has more than four bonds. EVER!

organic chemistry rules

3) Alkaline metals (Li, Na, ect) and alkali earth metals (Be, Mg, Ca, ect) can NEVER be negatively charged.  They will always be neutral or positively-charged ions in solution.

4)  Noble gases are NEVER a part of any organic molecule.  Because they have a full octet, they have very little reason to create a covalent bond.

5) Electrons ALWAYS flow from negative to positive.  This is a biggie.  And because of this, rule #6 exists.

6) Reaction arrows ALWAYS point from negative to positive.  Always point from the nucleophile to the electrophile.


– Carbon can have 4 bonds (neutral), 3 bonds (positive, negative), or even 2 bonds (carbene)

– Halogens USUALLY have one bond, but can occasionally have two.

– Nitrogen usually has 3 bonds (neutral), 4 bonds (positive) or 2 bonds (negative)

– Oxygen usually has 2 bonds, but can have only 1 bond (negative) or 3 bonds (positive)

– Phosphorous is USUALLY an oxophile, meaning if it can react with oxygen, it will.


This brings us to another point about knowing the common states of organic atoms.  This can really help you in solving organic chemistry if you know the normal state of organic atoms [this is a link to one of our favorite blog posts]

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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.  What is a strong nucleophile?  Check out these blog posts on strong nucleophiles and strong electrophiles.

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.




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?


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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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Know your strong nucleophiles [with chart]

What are strong nucleophiles?  

Strong nucleophiles: This is VERY important throughout organic chemistry, but will be especially important when trying to determine the products of elimination and substitution (E1, E2, SN1, SN2)reactions.  In fact, there is not a more important part of an organic chemistry reaction than the nucleophile and the electrophile.   So, let’s look at what makes strong nucleophiles.

There are generally three trends to remember when discussing how nucleophilic a reactant is:

1)      Size – Generally, the more linear and/or smaller the nucleophile, the more nucleophilic it will be.  This is because it can react at more sites and will not be sterically hindered if it is smaller or linear.

2)       Electronegativity– The more electronegative an atom is, the less nucleophilic it will be.   This is because more electronegative atoms will hold electron density closer, and therefore will be less likely to let that electron density participate in a reaction.  We see this in calculations and experiments that show nucleophilicity decreases as you get closer to fluorine on the periodic table (C > N > O > F)

3)      Polarizability– The more polarizable an atom is, the more nucleophilic it will be.   Polarizability is defined as the ability to distort the electron cloud of an atom, which allows it interact with a reaction site more easily.  Generally, polarizability increases as you travel down a column of the periodic table (I > Br > Cl > F)

Below is a table of relative nucleophilic strength.  This is relative because nucleophilic strength is also dependent on other factors in the reaction, such as solvent.


VERY Good nucleophiles


Good nucleophiles

Br, HO, RO, CN, N3

Fair nucleophiles

NH3, Cl, F, RCO2

Weak nucleophiles


VERY weak nucleophiles




free organic chem study guide


As shown above, as a general rule, the anion of a reactant will be a better nucleophile than the neutral form.  (i.e. RCO2 is a better nucleophile than RCO2H)

Step 2 is learning about the electrophiles.  Please visit our recent post on this topic –> electrophiles

For more information on this and other topics of organic chemistry interest, please visit organic chemistry


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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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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Organic Chemistry Help: Learn new chemistry almost anywhere

Did you know that there are 37 ingredients in a Twinkie?  Here is photographic proof of it.  Twinkie ingredients.  Now that you are a budding organic chemist, if you saw the list, how many do you think you would be able to identify?

Ok here is a quick hint and a fun way to study chemistry almost anywhere.

There us chemistry all around us. A good way to learn it is to take the products you use everyday and look at the ingredients list. Figure out which compounds you already know and try to visualize the structures in your head or determine why they are in there. Find a chemical compound that you have never heard of and go look it up later. You'll not only reinforce compounds that you already know but learn some new organic chemistry at the same time. On what products can you do this? Just about anything. You can learn in the shower from soap, shampoo or shaving cream. You can learn while in the kitchen from just about anything you might eat. (Ironically the hardest food to use this technique on are organic foods since there are so few byproducts in them) For more organic chemistry help, please go to organic chemistry.

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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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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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