Archive for the "Organic Chemistry General" Category

Studying for Summer Organic Chemistry

Posted on June 8th, 2015

One of the biggest challenges students can undertake is signing up for Organic chemistry in the summer.  How so?  Well, there are a few reasons.

First, the course time usually shrunk from 16 week to 8 weeks.  This means, longer classes and more frequent tests.  Secondly, the subject material is usually covered more quickly, but the content remains the same.  As such, students can feel overwhelmed and become exhausted studying the materials much more quickly than is typical.  But, we here at StudyOrgo have streamlined the process of studying organic chemistry mechanisms!

Our illustrative overviews with full mechanism descriptions and diagrams makes mastering any reaction in your class much easier.  And, with over 170 reactions, you’ll feel confident you’ll have everything you need to get the “A” in this course.  Here are a few tips for getting the right start to studying with help from StudyOrgo today!

  • Time management – Schedule your studying NOW! – Time management is the key to acing organic chemistry in the summer. 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. Think of it as a doctor appointment – you just have to do it!  Also, if you plan your studying ahead, you will be less likely to schedule something that gets in the way because you will already have penciled it in! Use your Smartphone calendar to send you alerts and reminders for your studying appointment.
  • Open your text book – Read the title and abstract on the first page of each chapter and check out the number of pages. It will give you a very quick idea of what you will be learning about in each chapter and how much material you will be covering.
  • Look at a syllabus – Remember, your syllabus is an official contract between you and the professor. They must disclose what you are required to learn and how you will be graded. Professors can remove requirements at will but cannot add them easily. Use this to your advantage! Highlight the contents or reactions of the book that will be required and use this to focus your attention on while studying over the summer course.
  • Read ahead – Before each class, glance at the chapter to be covered that lecture beforehand. Don’t try to understand everything, just pay attention to the major words and phrases used and the ideas. This will allow you to pay more attention during class because you will already know what is being said, now you pay attention to the details. Most people are scrambling to write down notes and drawings in class, but not really paying attention.  Try it yourself, look at your classmates at the next class for a minute or two, they are usually feverishly writing!
  • Sign up with StudyOrgo – The Editors at StudyOrgo have painstakingly reviewed and prepared the material in the most crystal-clear and “get-to-the-point” manner as possible. We consult students and ask for their opinion on whether they understand the material as presented. 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!

With a little time management and StudyOrgo, you will have no trouble getting an A in Organic Chemistry this summer!

Organic Chemistry of Lipids

Posted on May 11th, 2015

Lipids are a fundamental part of biochemistry and draw many analogies to reactions with alkenes and alkanes.  In this article, we will review some basics of lipids and their organic chemistry implications.  Many of the reactions with lipids are simple hydrocarbon reaction mechanisms covered in Organic Chemistry 1.  With over 175 reaction mechanisms, StudyOrgo is devoted to making organic chemistry reaction mechanisms easy to learn and points out common places where errors are made.  Sign up with today to get more in-depth coverage of common reactions for your next exam!

Lipids are any complex chain of hydrocarbons that may or may not contain additional functional groups. Some common classes of lipids are fatty acids and triglycerides, waxes, terpenes and steroids; examples of which are shown in Figure 1. 

Lipid Figure 1

Most lipids usually consist of a long hydrophilic tail coupled to a polar head group that undergoes reactions to elongate or shorted the hydrophobic tail.  We will cover some common organic chemistry reactions with each of these classes of lipids.

Complex Lipids – Fatty acids and Triglycerides

Complex lipids are capable of undergoing hydrolysis reactions.  The basic unit of a complex lipids are fatty acids, which are made up of a hydrophobic tail coupled to a carboxylic acid head group (Figure 2).  The length of the carbon chain denotes the lipid name.  In addition, the number of double bonds, or degree of unsaturation, also influences the name.  In biology, naturally occurring double bonds will always be found in the cis- configuration.

Lipid Figure 2

Hydrogenation of alkene groups to alkanes occurs at high temperatures, such as in deep fryers for cooking, and this side reaction leads to the isomerization of the double bond to the trans- conformation, hence trans-fatty acids.  These lipids are toxic in high quantities because they are unable to be metabolized by the cell, thus accumulating and undergoing oxidation reactions over time and theorized to promote inflammation and metabolic diseases.  Coupling of a fatty acids to the alcohol groups of glycerol forms the complex lipid, triglyceride (Figure 2).  This reaction occurs enzymatically in the cell but closely resembles the mechanism found in acid-catalyzed Fisher Esterification.

Lipid Figure 3

Simple Lipids – Sterols

Steroids are an integral part of cellular biology but are classified as simple lipids because they cannot be hydrolyzed (i.e. they do not have reactive carbonyl or carboxyl groups).  A lipid molecule having a tetracyclic shape in the arrangement similar to cholesterol is classified as a sterol.  Cholesterol serves as the building block of all steroids and substitution, addition and elimination of functional groups derives the variety of steroids found in the body. Cholesterol is synthesized from the 5 carbon lipid molecule isopentenyl phosphate.  Condensation of isopentenyl phosphate forms geranyl phosphate (10C) and farnesyl phosphate (15C) in a reaction mechanism that involves allylic carbocation and tertiary carbocation intermediates (Figure 3).  Condensation of two farnesyl phosphate molecules forms the 30 carbon intermediate squalene, which in several steps is converted to cholesterol.  Two important examples of steroids are the sex hormones found in humans, estradiol and testosterone, which regulate a wide range of biological functions.

Lipid Figure 4

Carbohydrates in Organic Chemistry

Posted on April 24th, 2015

Many organic reactions you encounter have very practical uses.  In this section, we will describe the organic chemistry of carbohydrates.  Sign up today with StudyOrgo to see more illustrations and easy explanations to make your Organic Chemistry studying a success!

What’s in the Name?

Carbohydrates, or saccharides, are molecules of 3 carbons or more which contain at least one carbonyl group and one alcohol group.  Carbohydrates containing an aldehyde group are referred to as aldoses while carbohydrates with a ketone group are referred to as ketoses. Like all organic molecules, stereochemistry is an omnipresent consideration.  Recall that chiral, non-superimposable, mirror images will rotate plane-polarized light to the left or right, referred to as S and R respectively.  In carbohydrate chemistry, left- and right- rotation is referred to as L (levorotary) and D (dexorotary), but their meanings are exactly the same!  Remember that chirality is a key to life; as a matter of fact animal cells are only capable of utilizing the D-isoforms of saccharides while the L-isoforms are not metabolizable!

The simplest carbohydrate is glyceraldehyde (C=3) which has 1 stereocenter, therefore it has two enantiomers.  C=4 carbons have 2 stereocenters and two different arrangements of the OH groups, named Erythrose and Threose (diastereomers), but each has a mirror image (enantiomers), thus resulting in 4 stereoisomers. C=5 carbons has 3 stereocenters, thus giving 8 stereoisomers, the 4 diastereomers referred to as ribose, arabinose, xylulose and lyxose. Remember, for each OH arrangement, only 1 mirror image (the enantiomer, D or L) exists!

carbohydrate 1

Cyclization of Carbohydrates

Recall hemiacetal formation, which is the reaction of aldehydes or ketones with an alcohol to produce the hemiacetal functional group.  You will also recall that inter-molecular hemiacetal reactions are unfavorable.  However, intra-molecular hemiacetal formation, which is possible in carbohydrates, is very favorable (Figure 2). Thus, carbohydrates are typically drawn as a Hayworth projection. The aldose or ketose when cyclized is renamed to resemble the molecule pyran (5 carbon cyclized ether) or furan (4 carbon cyclized either).  Thus, for D-glucose the cyclized version is renamed D-glucopyranose to indicate a cyclic structure.  The ‘pyran’ is usually dropped in the vernacular of biochemistry but is an important distinction to make for the exam!

carbohydrate 2


The alcohol formed from the hemiacetal reaction is an important functional group in the organic chemistry of carbohydrates.  This carbon center, usually at position C1 or C2, is referred to as the anomeric position. It is also a stereocenter, and the resulting enantiomers are referred to as anomers.  When the OH is pointed above the plane of the ring, it is referred to as the beta- configuration while the OH pointed below the ring is the alpha- position.  All monosaccharides contain an anomeric carbon!

carbohydrate 3

Reducing Sugars

Equilibration back to the aldose or ketose makes the carbonyl susceptible to oxidation by reagents, such as silver nitrate, the main component of Tollen’s Reagent.  This reaction converts the carbonyl in saccharides to a carboxylic acid.  In the process, silver precipitates to form a mirror-like residue on the beaker. Thus, any saccharide that tests postive in this reaction must have an anomeric position that can equilibrate to the aldose or ketose configuration and is said to be a reducing sugar. Reducing sugars are useful carbohydrates in making polysaccharides, or polymers of carbohydrate units involving the formation of glycosidic bonds (Figure 4, sucrose red oxygen). However, when the anomeric position between two saccharides are linked together, the anomeric postion (also known as the reducing end) on both sugar units is unavailable.  Take for instance sucrose (table sugar); it is a disaccharide of glucose and fructose.  However since both reducing ends are used in the glycosidic bond, they will not react with Tollen’s Reagent, thus sucrose is said to be a non-reducing sugar.

carbohydrate 4

Learn SN1, SN2, E1, and E2 quickly with our videos

Posted on April 22nd, 2015

Nucleophilic substitution and elimination reactions can be daunting. There are so many differences and similarities that it can be difficult to keep everything straight. Our Chief Educator, Dan, has put together four videos aimed at teaching you these four reactions quickly and easily.

Take a look:





Epoxides: Formation and Utilization

Posted on February 27th, 2015

Epoxides are useful functional groups in organic chemistry for generating reactive centers. Many drugs, both beneficial and harmful, rely on the process of epoxidation to become biologically active.  In this article, we will review some of the concepts of epoxidation and give you a preview of the hundreds of reactions explained with clear depictions when you sign up for a membership with StudyOrgo!

There are two processes, ring closing- (epoxidation) and ring opening- reactions. Epoxides contain an oxirane, which is a 3 membered ring that contains an oxygen atom.  Preparation of epoxides require a double bond across which the oxygen will be added across the C-C bond to form the oxirane ring.

Ring-Closing Reactions:

Formation of an oxirane ring can be accomplished in 3 ways starting with an alkene reactant. The use of the following peroxides is a common way to prepare an epoxide.

  • Peroxy Acids

***Memorize both of these reagents– if you ever see them- think epoxides!

epoxide 1

  • The third method requires hydrobromination across the double bond to form a halohydrin. Reaction with a strong base then leads to intra-molecular SN2 reaction that produces the epoxide.

epoxide 2

Ring-Opening Reactions:

Reaction of epoxoides with any strong nucleophile leads to ring opening and formation of an alcohol via an inter-molecular SN2 reaction. Nucelophiles such as OH, OR, SH, Grignard Reagents and LAH will all attack the epoxide at the least sterically hindered position to break the ring. A practical example of ring opening reactions is the use of ethylene oxide to sterilize medical equipment.  Microbes present on the surface of the equipment are exposed to ethylene oxide whereby DNA, RNA and proteins contain many -NH2 and -OH groups to serve as nucleophiles that will react with the epoxide.  The result is an alkylated group, which will interfere with cell function and induce cell death, known as apoptosis.

The second example explains the organic chemistry of the widely-used monomer Bis-Phenol-A, which has drawn attention for its potentially carcinogenic properties, is reacted with the epoxide, epichlorohydrin, to form polymers used in many plastic products. Note that upon ring-opening of the epoxide in Step 1, a halohydrin is instantly formed and can is further reacted in Step 2 with NaoH in a ring-closing reaction to regenerate the epoxide for another round of catalysis in Step 3, so a long strand of the BPA polymer is formed.

epoxide 3


Sign up with StudoOrgo today to get more explanations and clear-cut examples of the mechanisms required in your Organic Chemistry 1 & 2 course today!