Tips on Sigmatropic and Electrocyclic Reactions

Posted on May 18th, 2016

One of the most common difficulties in Orgo 2 is the concept of sigmatropic and electrocyclic reactions.  Both of these reactions involve conjugated pi bond systems, which are multiple, adjacent carbon atoms with connected pi bond orbitals.  The Greek word sigmatropic literally means “sigma(bond) changing”, thus when presented with a conjugated pi bond molecule where bonds are broken and formed, the driving force of this reaction is carried out by moving the pi-bond system around the molecule.  Two types of sigmatropic reactions are common for this class.  First is the Cope rearrangement.  This is also referred to as a [3,3] sigmatropic rearrangement.  Many students struggle with with nomenclature, especially since the [x,x] nomenclature is most often presented on tests.  What does it exactly does [3,3] or [1,5] mean?

Lets look at a few examples.  Below is a typical Cope Rearrangement with [3,3] sigmatropic rearrangement.  We see that the reactant has 2 pi bond (or 4 pi electrons) in a pseudo-cyclic arrangement. Right now, each alkene has one substituent that is not an H.  if we move the pi-electrons around the ring, we can form a resonance structure (middle molecule) which is a complete ring.  The product is to break the sigma bond in red and form a sigma bond in green.  But why are there three arrows (meaning 6 electrons) involved in the mechanism?  This is because while in the reactant the red bond electrons are sigma, when the molecule rearranges, they will be used to form a new pi bond, while the reactant pi bonds will donate electrons to become the green sigma bond. Now one of the alkenes has two substituents, which is more favorable and drives the reaction to the right.

A question that comes up frequently is what the numbering of the rearrangement means?  To determine this, there a few easy steps to follow;

  1. Identify what bond will break and what bond will form.
  2. Draw an imaginary plane that intersects these two bonds.
  3. Count the atoms starting from the top of the plane from where the bond was broke to where it forms. This is the first number [3.x]
  4. Count the atoms starting from the bottom of the plane from where the bond was broke to where it forms.  This is the second number [x.3]
  5. Placing them together, we can see that a [3,3] sigmatropic rearrangement means a new bond is formed between atom 3 above and atom 3 below the imaginary plane.

The same is true for non-carbon atoms in the ring.  The second example looks at a [1,5] sigmatropic rearrangement of hydrogen (also called [1,5] hydride shift).

  1. Identify what bond will break and what bond will form.
  2. Draw an imaginary plane that intersects these two bonds.
  3. Count the atoms starting from the top of the plane from where the bond was broke to where it forms. In this case, there is only one atom, the hydrogen.  This is the first number [1.x]
  4. Count the atoms starting from the bottom of the plane from where the bond was broke to where it forms.  This is the second number [x.5]
  5. Placing them together, we can see that a [1,5] sigmatropic rearrangement means a new bond is formed between atom 1 above and atom 5 below the imaginary plane.

sigmatropic article 1

In cases where oxygen is present as an ether, the name of the reaction is changed to Claisen Rearrangement.  However, the mechanism is the same.  The aldehyde or ketone product is almost alway preferred to the ether reactant shown here.

sigmatropic article 2

 

Another question that is typically a major stumbling block of students is the rules for choosing reaction conditions for electrocyclic reactions.  This refers to the rotation of pi bonds  to form new sigma bonds or the rotation of sigma bonds to form new pi bonds.  The two atoms can rotate their orbitals in such a way that they rotate in the same directions (conrotory), which gives trans- orientation, or in opposite directions (disrotory), which gives cis- orientation.  The main point is that the substituents on the these atoms will be in different stereochemical arrangements.  When a chemist wants to choose the correct stereochemical outcome of the molecule, you have to choose the right conditions to get the substituents of these electrocyclic atoms in cis- or trans- to each other.

 

Below is a convenient table to help you identify the right condition for the reaction presented to you.

electrocyclic

 

 

Carboxylic Acids and their Derivatives

Posted on April 18th, 2016

Here is a look at a reaction directly from our proven organic chemistry flash card system:

Carboxylic Acids and their Derivatives

Esterification of Acid Chloride

Overall Big Picture: In this reaction, an acid halide is reacted with an alcohol to give an ester.

Acid Chloride + Alcohol → Ester

Key Tip: A mild base is required to drive the reaction forward.

Key Comparison: This reaction is only possible due to the high reactivity of acid halides for nucleophiles, even weak ones like alcohols.

Mechanism Hint: Collapse of the addition intermediate is propagated by deprotonating by pyridine, which helps to drive the reaction forward.

Note: When this reaction is carried out using p-toluensufonyl chloride (tosyl group), this reaction is a good protecting group for alcohols.

First window: acetyl chloride

Middle window: alcohol, pyridine

Last window: methyl ester

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How to approach synthesis problems

Posted on February 9th, 2016

Q: “I am in organic chemistry 2 and I am trying to learn how to predict the products.”

One of the most challenging, but ultimately the main goal, of organic chemistry is to take an abundant, cheap starting reactants and transform it into a biologically active or synthetically useful product.  In the two semesters of organic chemistry, you will learn reactions that will produce all of the functional groups that give molecules these useful properties. But as a chemist, it is very importantly to accurately predict how and in what yield these reactions will produce you desired products.

The stakes seem higher when you are given less than 2 hours to complete several multi-step synthesis problems that often ask to identify not only reagents but the mechanism of each step of the reaction.  We here at StudyOrgo have compiled advice and guidance for learning to tackle these problems.

  1. Relax!
  2. Understand that each step in a synthesis reactions can be broken down into two basic types of reactions;
    1. Change in the carbon-carbon skeleton: Take a look at the starting material and the final product. Count the carbons, is there a difference in number?  If so, then you will need a carbon-carbon bond breaking or addition reaction.  There are only a few examples of these reactions so that instantly narrows down reactions you have to focus on.
    2. Change in the identity or location of a functional group: This is the most common synthesis question. Remember, that the pathways from one functional group to another are limited.  Set up a reaction roadmap or use included with your StudyOrgo membership to help you memorize what reactions can be used to get you to your final functional group.
  3. There are often times MANY routes to get to a final product. ALL OF THEM ARE CORRECT, if in fact the route is possible.
    1. HINT: Professors will only ask you to use reactions they have covered in class. Make a list and indicate what the reaction does to help you memorize the products.
  4. Sound out the problem. Often time students have a viable synthesis approach, but get held up at one or two places and just leave the entire question blank. Remember, it is multistep, which means there are many places to get points!  Draw out what you know.  Worst-case scenario: you get partial credit.  Best case scenario: you realize what reaction is next and get full points!!
  5. Practice, practice, practice! Make sure to perform all of your practice problems assigned to you for each chapter.  It takes a lot of time and effort, but likely these examples will be used by your professor.  Also, the more examples you see the less surprises will be on the exam!
  6. Sign up with StudyOrgo for help! The Editors at StudyOrgo have spent numerous hours reviewing and preparing the material in the most crystal-clear and “get-to-the-point” manner as possible. We provide quick descriptions and in-depth mechanism explanations. Many of our reaction have multiple examples, so you can learn and then quiz yourself in our website! For the student on-the-go, we have also developed a mobile app (iOS and Android) provides all the functionality of the website! All of these benefits are included in your StudyOrgo membership!

 

 

Epoxide Reactions

Posted on February 3rd, 2016

Many students taking Orgo 1 have commented there are a few types of reactions the professors save to the end of the semester and cover quickly and “gloss” over or sometimes skip all together in the interest of time.  However, in Orgo 2, you will be responsible for all of the reactions necessary for multi-step synthesis (starting product known to get to unknown final product) and retrosynthesis (product known to get to unknown starting material) reactions.  We at StudyOrgo don’t want you to get stuck on trying to cram for exams by studying reactions that were poorly covered in your class.  In this article, we focus on epoxide formation and epoxide ring-opening reactions because of their usefulness in synthesis and industrial application.

Epoxide Formation

In order to form an epoxide, a electron-rich reagent is required, such as an alkene.  Formation of the epoxide occurs in the presence of a peroxide reactant, such as MCPBA or DET.  The choice of reagent depends on the stereo-specificity desired from the reaction.  MCPBA is used to add the epoxide symmetricaly across the double bond, so that substituents that are cis- or trans- remain in this configuration.  The Sharpless asymmetric addition allows the researcher to choose a stereoisomer of DET, referred to as (+) and (-).  This reagent allows for the attack of the peroxide intermediate on only one face of the alkene, allowing for the production of nearly pure enantiomeric excess product, generally >98%!

epoxides article 1

Ring-opening Reactions

Many of you have probably hear of epoxy-glue, which is a very strong binding agent.  The process usually involves mixing two reagents and you must quickly apply the mixture to the broken items before the expoxy hardens.  One tube will contain the resin, or epoxide, while the other contains the “hardening” agent, which is the nucleophile that will attack the epoxide.  In a ring-opening reaction, a molecule such as TETA, which contains 4 amino groups, will attack 4 equivalents of oxirane to produce a complex polymer, which is the basis for a strong glue.  Changing the size and complexity of the epoxide can allow for flexibility of strength, thermostability and rigidity!

epoxides article 2

We here at StudyOrgo have devoted countless hours to preparing complex reaction mechanisms in simple and easy-to-understand manner to help you maximize your studying.  Sign up with StudyOrgo for detailed explanations of epoxide reaction mechanisms and other essential Orgo 2 reactions today!

 

Preparation Tips for Spring Semester Organic Chemistry

Posted on January 17th, 2016

 

Going into the spring semester, you might feel like you know what Orgo 2 will be like.  However, the second semester of organic chemistry has a very fast pace, anywhere between 50-100 reactions will be presented. You’ll be responsible for all of them!  Sign up with StudyOrgo today to help you get all of your reactions mechanisms and descriptions instantly!

  • Read ahead – The first week of Orgo2, read two chapters to get yourself ahead of the class. Don’t try to understand everything, just read the text and try to understand the big ideas. This will completely change the way you pay attention in class and allow you to spend more attention and ask questions about the details in class instead of scrambling to write down notes and drawings.
  • Attempt ALL homework problems – When tutoring students, they are often intimidated when we ask them to try sample problems.  But after a few examples, every student does them better and better with each new problem.  Some students have even made comments such as ‘why didn’t I do this sooner?’  We were at StudyOrgo agree!  It takes a lot of time, but practicing the problems will make it easier for the quizzes and tests.
  • Look at a syllabus – Remember, your syllabus is an official contract between you and the professor. Professors are required to disclose what you are required to learn and what grading rubric will be used. Professors can usually remove requirements (to the delight of the students!) but cannot easily add them. Use this to your advantage! Highlight the contents or reactions of the book that will be required and use this to focus your attention when studying this semester.
  • Schedule your studying! – Now that you know where the book is and a rough idea of what you are responsible for learning from the syllabus, take a calendar and divide the time you have to each test by the number of chapters. Schedule 2-3 hours a week to study and DON’T SKIP OR RESCHEDULE. Use your Smartphone calendar to send you alerts and reminders for your studying appointment.
  • Sign up with StudyOrgo – The Editors at StudyOrgo have compiled detailed mechanisms and description of over 175 reactions in the most crystal-clear and “get-to-the-point” format possible.  Many of our reaction have multiple examples, so you can learn and then quiz yourself in our website! For the student on-the-go, we have also developed a mobile app (iOS and Android) provides all the functionality of the website! All of these benefits are included in your StudyOrgo membership!

With good time management and help from StudyOrgo, you can earn a top grade in your Orgo 2 class this semester!