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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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Keto-Enol Tautomerism [with free study guide]

Keto-Enol Tautomerism


Keto-Enol Tautomerism is a process where an equilibrium occurs between the keto form (ie a normal-looking ketone) and the enol form (a double bond adjacent to an alcohol) of a carbonyl, acheived through the movement of atoms and breaking of single bonds.

Spoiler alert: In most cases, the keto form is highly favored.

What is the keto form of a carbonyl? The keto form is what you are used to looking at. It is any normal-looking aldehyde or ketone, in which there is a carbonyl and hydrogen atoms alpha to the carbonyl.  See below:

What is the enol form of a carbonyl? The word “enol” can be broken down into two parts: “en” (pronounced “een”) as in part alkene, and “ol” as in part alcohol. The two parts, the alcohol and alkene, come off of the same carbon atom. See below:

What is this crazy thing called tautomerization? Tautomerization is a process where single bonds are broken and atoms are rearranged to give a different structure.  This is different from resonance structures, where you NEVER break a single bond. In Keto-Enol Tautomerism,  a carbonyl double bond is broken,  an alkene double bond is formed, and a hydrogen atom migrates from the alpha carbon to the oxygen atom, forming an alcohol.

keto-enol tautomerism

What is this equilibrium you speak of? Remember, that energy within the solution can cause structures to form which aren’t the most thermodynamically favored. This is what is happening here. There is an equilibrium between the keto and enol form, almost exclusively favoring the keto form. However, the enol form does exist in solution.  The ratio of keto to enol forms depends on several factors, which we will discuss further below.

When is the enol form more favored or the major form?  We think there are four situations where the enol form is more favored (but not necessarily the major form) you should learn.

  • Situation 1: When you get conjugation out of it.  Conjugation will mean more enol form.

  • Situation 2: When you get increased hydrogen bonding.  (and in this case, some conjugation too)  This one is sweet because the hydrogen-bonding makes a six-membered ring.

  • Situation 3: When you can get aromaticity out of it.  In this case, there is nothing but the enol form.

  • Situation 4: If you can get a more substituted alkene.  There will be more of B in the enol form than A, but still not a ton of B.  There will be more of B in the enol form in its equilibrium because tetra-substituted alkenes are more stable than di-substituted.





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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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Epoxidation of Alkenes [with free study guide]

Epoxidation of Alkenes

Somewhere in one of your exams, you will see at least one question on epoxidation of alkenes.

The reaction:  What is epoxidation? An epoxide is a 3-membered ring containing two carbon atoms and one oxygen atom. It is interesting because it is easily opened due to small ring strain and due to the electronegativity of the oxygen atom.


The reagents and starting materials:

1) What is an alkene?  An alkene is an unsaturated hydrocarbon containing at least one double bond.


2) What is epoxidation of an alkene? This is the reaction where an alkene is subjected to a peroxyacid to convert it into an epoxide. Another way to say it is epoxidation is the electrophilic addition of oxygen to the double bond of the alkene.


3) What reagents can you use to create the epoxide? Generally, peroxy acids are used in this electrophilic addition to the alkene. There are several types of commonly used peroxyacid such as proxy trifluoroacetic acid, peroxyacetic acid, hydrogen peroxide, and mCPBA.



The mechanism: The mechanism for the reaction is relatively complex.   While it is considered a single step reaction, it involves several changes. The double bond is our nucleophile and attacks the more electrophilic oxygen. This breaks the weak oxygen-oxygen bond and creates a new carbonyl. Once this carbonyl is formed, rearrangement occurs and the more electrophilic oxygen is released to become the oxygen of the epoxide.

mechanism of epoxidation

The stereochemistry: The stereochemistry associated with this reaction is interesting and important. As the reaction can occur on a cis or trans alkene, we see the two different products come from these two different starting materials. The oxygen can only attack from one face of the alkene. This means that the stereochemistry of the alkene is retained. Translation: if you start with a cis alkene you will get a cis epoxide. If you start with a trans alkene, you will get a trans epoxide.

epoxidation of alkenes

Further, remember that if you start with a di or tri-substituted alkene, you very well may create new stereocenters. However, if you remember the golden rule of chirality, you will know that  you need to start with chirality in order to finish with it. These alkenes are not chiral to start with, therefore we will end with a racemic mixture. If there is some chirality in the molecule, somewhere near the double bond then that chirality can influence which face the peroxyacid is attacked from, but will not exclusively give a chirally pure product.

The reaction the reaction is versatile, and works on many different alkenes. Please remember that the reaction will not work on the double bonds of an aromatic compound.

Some examples:






We rate the importance of this reaction, the epoxidation of alkenes, as four beakers out of five.



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Organic Chemistry Help: Deciphering an NMR [with study guide]


Happy New Year!  It has been a while since we have put a new organic chemistry post up, so I thought I would put a little guide up now that finals are over. 


The question is:  How did you decipher an H1 NMR spectrum?  Well, here is a good, uniform way to tackle the problem. 


Step 1: Calculate the degree of unsaturation in the molecule.  This is sometimes called the Sum of Double Bonds and Rings or SODAR.  You will most times be given a molecule formula, and can calculate your total number of double bonds and rings in the molecule using the formula (2#C + 2 – #H – #X + #N)/2 where


            #C = the number of Carbons

            #H = the number of Hydrogens

            #X = the number of Halogens

            #N = the number of Nitrogens


In this, you do not count the oxygen or sulfur atoms.  For example, the molecular formula C6H6NOCl would be (2*6 + 2 – 6 –1 +1)/2 = 4, meaning that there are 4 double bonds and/or rings.  It is helpful to remember that benzene rings equal to 4 on the SODAR scale, so if you have a SODAR that is 4 or larger, think benzene ring.


Step 2: Look for arene protons.  The number of protons between 6ppm-7.5ppm, known as the AR region, can give many clues to your molecule.  A mono-substituted benzene ring will have 5 protons in the AR region.  A di-substituted benzene will have 4 protons in the AR region.  However there are even clues to what type of di-substituted benzene it is.  If the peaks in the AR region are 2 perfect doublets, it is most likely para substituted.  If you have a singlet in the AR region, you most likely have a meta-substituted benzene.  If you just have a mess, it is most likely ortho substituted. 


Step 3: Look for the 2 A’s, aldehydes and alcohols.  This is actually simpler than it sounds, and can give you some nice clues.  Aldehydes are sharp singlet peaks that show up past 9ppm.  Alcohols are broad singlets that can show up anywhere in the spectrum, but will “exchange” with D2O, meaning that they will disappear if D2O is added.  Most organic chemistry profs will signify this by writing “exchange” over your spectrum.


Step 4:  Add up the integrations in your spectrum and make sure it equals the number of protons that you have.  For example, if you have 10 H’s in your formula, but can only have an integration equal to 5 on your spectrum, you need to realize that each integration is equal to 2 protons.


Step 5: Start to make fragments and then add up the fragments.  Using the integration and splitting of each peak, you can start to write down fragments of the molecule.  For example, if you have a singlet with an integration of 3, you know that you have a methyl group (3 H’s) next to something with no protons.  If you have a doublet with an integration of 2, you have a CH2 that is next to a CH.  Once you have all of your fragments, start to piece them together and you will be figure out what your molecule is. 

 For some good practice tests, please see organic chemistry.






Newman Projection Practice Problems [with free book]


Newman projection practice problems


When looking at Newman projection practice problems, there are a few areas that we need to make sure that we emphasize so you see the entire range of problems that might appear on an exam. First however, we should do a brief review on Newman projections. To see a full review of Newman projections, see this previous blog post. Briefly, Newman projections are a way to view simple organic molecules by looking at down the axis between two carbon atoms. We show the carbon atoms as little balls and the substituents as sticks coming off those balls at 120 degrees away from each other. There are three primary configurations a Newman projection can be in: staggered, eclipsed, and gauche. Below you can see examples of each one of these.

Now that we know what a Newman projection is, let’s look at what the most common types of questions you will see are:


Problem #1: Can you draw a Newman projection?  Draw the Newman projection of butane.

This is the most basic of Newman projection practice problems. All you have to do to master these problems, is find out where the axis of interest is. Please note, this is much different than the axis of Evil.

Generally, the main axis, or axis of interest, or carbon-carbon bond of interest will be a central carbon bond in your molecule. For example, in butane the most common axis for Newman projection is the C2-C3 axis. Of course, you can draw a Newman projection down any bond axis, but the C2-C3 axis is the most beneficial to view in a Newman projection.


Below are some more questions to help you practice this.


Problem #2: Do you understand relative energies? Which are the lowest and highest energy confirmations of a Newman projection?


If we take what we learned above, with respect to how to draw a Newman structure and the types of conformations that exist, this problem becomes much easier. For the purposes of undergraduate organic chemistry, 98% of the time the lowest energy structure is going to be a staggered structure where the largest groups are 180 degrees away from each other. This is the lowest energy conformation because there is limited torsional and steric strain. We will go into torsional and steric strain more below. Try these practice problems to see if you can come up with the lowest energy conformation of these Newman projections.


Problem #3: Do you understand strain? Is there torsional or steric strain?



There are two types of strain that can be seen using a Newman projection. The first is steric strain. This is much more common in other types of organic chemistry problems, and occurs when two large groups are near each other. With respect to Newman projections, anytime two groups that are a methyl size or larger are near each other there is steric strain. Hydrogen-hydrogen interactions do not really lead to steric strain like a methyl-methyl interaction will.


The second type of strain is torsional strain, which occurs when bonds overlap. For the purposes of Newman projections, anytime we have an eclipse conformation there will be some torsional strain. Armed with this knowledge, let’s look at some more problems.


Practice problem #4:  Do you understand relative energies? Draw the energy diagram for a Newman projection:


Energy diagrams show the relative energy of a molecule compared to rotation about the axis of interest. Generally, these start at 0 degrees and rotate through the entire molecule. This can then be graphed showing which parts and bond angles about the axis of interest are more or less stable. Because this diagram is relative, we will make some educated guesses when we draw it out. To make one of these energy diagrams, we have to have a good idea ahead of time of what the lowest and highest energy conformations are. To do it thoroughly we are going to walk through the conformation and check the relative energy every 60°. Since there are 360 degrees in a full rotation, that means we will have six different energy points to plot on our diagram per molecule. Here is a good example of what one of those will look like.

Newman projection practice problems #5: What about advanced Newman projections? Draw cyclohexane as a Newman projection.


Students should realize the Newman projections are not just confined to linear molecules. Newman projections can be used in cyclic molecules also. Some professors like to test this concept using cyclohexane. With a little bit of practice, this can be done relatively simply. The main thing to remember is that in cyclohexane’s Newman projection there are two axes of interest.



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Alkane Formula [with free study guide]


The Alkane Formula


Before we can answer the question of what is the alkane formula, we have to ask ourselves what is an alkane. An alkane is a simple hydrocarbon containing carbon and hydrogen single bonded to each other, with a carbon backbone. Any molecule with this structure is going to have the formula CnHn+2, where n is any integer. Let’s look at some examples of this:






Please note, that this formula doesn’t tell us anything about the structure of the alkane, it only tells us that is fully unsaturated. For example, both pentane and 2,2-dimethylpropane will both be fully unsaturated and have the same molecular formula, but completely different structures and physical properties therefore we have to be very careful not to make assumptions about the structure of an alkane just based on its formula.

It’s a nice trick to know that any time you see a molecule with the formula CnHn+2, you know it is a fully saturated hydrocarbon, meaning that there are no double or triple bonds only single bonds. The degree of unsaturation, or “some of double bonds and rings” (SODAR) can be expressed using a similar formula. Here is a great post discussing the SODAR formula.


A quick rule of thumb to be able to determine if a molecule is saturated or not is just to ask if there are more than double the number of hydrogens as compared to carbon in the molecule.  For example, if you have a hydrocarbon with the formula C5H12, we know that there are more than double the number of hydrogen therefore this is saturated. If we have a structure with the formula C5H10, there are only double the number of hydrogens therefore this is unsaturated at some point in the molecule. What this little rule of thumb doesn’t tell us is where that unsaturation is or what type of unsaturation it is, a double bond or a ring.

Want some more background on alkanes?  Here is a good alkane post.



Check out this model kit and DVD


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Organic Chemistry Klein Textbook Review [Bonus Free Study Guide]

Organic Chemistry Klein


Today, we take a look at the organic chemistry Klein textbook, one of the most popular organic chemistry textbooks on the market right now. Written by David Klein, the book is now widely used in many undergraduate organic chemistry courses and is the number one textbook for organic chemistry on Amazon right now. While the 3rd edition is the most recent, the 2nd edition is still wildly popular.  See it on Amazon here.

But why is this book so widely used? What is so great about it? Let’s take a look.


The pros:

1) This textbook has a lot of practice problems. And when I say a lot I really mean a lot. As we noted in our survey of organic chemistry professors, they said the number one way to study was using practice problems and practice exams. The Klein book definitely gets this right. Further, the practice problems are placed after each concept is presented. This makes the structure of the textbook really effective, as it reinforces the topic immediately after it’s presented. Kudos to Professor Kline for constructing a textbook with this in mind.

2) Professor Klein has a great writing style. Many students enjoy the way his books are written and have described it as semi conversational, and very understandable. As organic chemistry can be a very confusing concept, the ability to write in this manner is highly commendable. This is definitely one of the main features of this book. I don’t know if there is a more understandable textbook on the market.

3) The “medically speaking” sections are a nice little bonus. Not only do they make organic chemistry more interesting and demonstrate its applicability in the real world, it keeps our med school students and biology friends interested in our science.






1) I have seen complaints online that there are errors in the textbook. While errors are not completely uncommon in organic chemistry textbooks, I have not personally found any of these errors myself in the Klein textbook. That doesn’t mean they don’t exist, it just means I didn’t see them when I read the textbook. Some of these complaints may be from students who don’t understand the concept completely, or got bad information from a tutor. I don’t even know if I should call this a con, but I wanted to add it in there since there were so many complaints about this online.

2) A big drawback is that you also need to purchase the solutions manual if you want to get all the answers to all the practice problems. The textbook itself is expensive enough, but then to throw on the expense of a solution manual is definitely another drawback.

3) Finally, some students have complained that the textbook is not as comprehensive as it could be. Some students actually say the Solomon organic chemistry textbook is a nice companion to this book as Solomon is more comprehensive. (For the record, I would not suggest buying two organic chemistry textbooks to complement one another). Some students don’t actually think the fact that Kline is less comprehensive his actually a problem. I can go either way on this. If indeed you don’t think Klein is comprehensive enough, there are plenty of other resources on the internet to complement what you learn in the Klein book (see below for an example). I don’t think any student should ever rely solely on one source of information in order to learn a very complex topic, such as organic chemistry. We always think it is better to buy some sort of supplemental organic chemistry book (usually at a far cheaper price) to round out your organic chemistry education.

Overall, we really like organic chemistry Klein, and give it our highest recommendation.


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5 Cardinal Rules of Carbon in Organic Chemistry


If you haven’t noticed by now, carbon is the most important atom in the organic chemistry world. It is all about carbon chemistry.




Here’s a hint: if it doesn’t have carbon in it, it is most likely not an organic molecule. Carbon is the basis of everything in this class. In some cases carbon will be a nucleophile, and in others it will be an electrophile. If you’re just starting out, there are some things you should know about carbon that will make your life a lot easier through your organic chemistry class.


  1. Carbon is the most important atom in the organic chemistry world.  I think we have sufficiently emphasized this point now.


  1. The sp3 carbon atom is a tetrahedral molecule with bond angles at exactly 109.5 degrees.


  1. Carbon atoms can be hybridized in three separate ways. sp, sp2 and sp3. sp3 hybridized carbons are seen in alkanes. sp2 hybridized carbons are seen in alkenes, and sp hybridized carbons are seen in alkynes. See below for a good picture of the bond angles for each.




  1. Carbon usually has four bonds to it. It can sometimes have three bond, and in rare circumstances even have two bonds. It will never never never never never have 5 bonds. Did I say never enough times? Seriously, don’t ever put 5 bonds to carbon please.



  1. Chains of carbon are called hydrocarbons and really only do two things. They are solvents, and they can be burned. That’s really about it.  This is because there is not a huge difference in electronegativity between carbon and hydrogen. Therefore it is not a polar bond, which means it doesn’t have polarized electrons which facilitate chemical reactions. This makes hydrocarbons very boring and non-reactive. Nonpolar, boring nonreactive molecules are great nonpolar solvents. But other than that they really don’t do much. There are ways to activate the C-H bond to do chemistry, but most of those are beyond the scope of undergraduate organic chemistry.  The exception is free radical halogenation of an alkane.


We are huge fans of molecular modeling kits to help you visualize the carbon atom and other atoms you will see in this class. Here is our favorite molecular modeling kit, which we just happened to create. It comes with a DVD which has two hours of instructional videos on it.


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