Archive for the "Organic Chemistry General" Category

How can I tell if a hydrogen is a wedge or a dash in a chair skeleton?

Posted on March 19th, 2017


“How can I tell if a hydrogen is a wedge or a dash in a chair skeleton?”

Here at StudyOrgo, we frequently get questions about topics in organic chemistry that are usually quickly covered, poorly described or expected that you know from previous courses.  These concepts are really important to understanding the more complex topics to come.  In this article, we will cover the concepts of stereochemistry descriptions using bold and wedged bonds.  This is just a preview of the detailed topics and materials available with your membership to  Sign up today!

The first thing we have to do is determine is how you want to orient you molecule.  Let’s take (1R, 2R) 1,2-dimethylcyclohexane for example.  If we orient the molecule to have the methyl groups on the right side, we see that we have two stereocenters available.  But the current drawing doesn’t indicate the stereochemistry yet.  That’s what the bold and hashed bonds will indicate.

Next, we have to visualize the cyclohexane ring in the chair conformation.  Remember, that the skeleton image shown above is more conveniently drawn, but loses the 3rd dimension information, so you have to put it back in the chair to determine which should be bolded and which should be wedge.

Next, we have to confirm that that the stereochemistry is correct.  To do this, you need to practice selecting most important substituents and rotating to assign stereochemistry.  Follow along with the examples below, using the blue and pink carbons shown.

At this point, you should be able to see how the hashed and bolded bonds are now appropriately drawn.  The pink stereocenter will be bolded, suggesting it is above the plane of the ring and the blue stereocenter will be hashed, suggesting it is below the plane.  Drawing the Newman Projection down the red bond shows that the methyl groups are “anti” to each other, making this a stable conformation.



I’m trying to figure out if it is an enantiomer, diastereomers, structural isomer, or meso compound.

Posted on March 7th, 2017

“I have two compounds that have the same substituents but they arranged different, I’m trying to figure out if it is an enantiomer, diastereomers, structural isomer, or meso compound.”

Here at StudyOrgo, we frequently get questions about topics in organic chemistry that are usually quickly covered, poorly described or expected that you know from previous courses.  These concepts are really important to understanding the more complex topics to come.  In this article, we will cover the concepts of stereochemistry to review the basics and look at some specific examples.  This is just a preview of the detailed topics and materials available with your membership to  Sign up today!

Structural isomers, or constitutional isomers, are molecules with the same chemical formula but different connectivity, they literally do not look alike.

Stereoisomers refer to molecules with the same chemical formula (i.e. same number of atoms) and geometrical arrangement (i.e. same connectivity) that are not superimposable on each other.  They frequently will be described as “R” or “S” configuration


For a carbon center (referred to as a stereocenter), this requires bonding to four different substituents!  If they are mirror images, they are enantiomers.  If they are not mirror images, then they are diastereomers.  Remember, you can use R and S configuration can help distinguish this.  R,R would be the enantiomer of S,S.  But both R, S and S,R are the diastereomers of R,R.

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Compounds that contain stereocenters but have a plane of symmetry across them (such that they have a mirror image of itself somewhere) are referred to as meso compounds. Take a look at tartaric acid, it has two stereocenters but the blue box represents an axis of symmetry that makes the compound meso.



The usefulness of this is that proteins (the drug targets) are also chiral, so they need chiral drugs to affect them.  If the compounds are not chiral, they will not interact with the proteins correctly.  For synthesis, if the compounds are not chiral, they will not rotate plane polarized light, and will be called “optically inactive”.

A few tips:

  1. If you only have one stereocenter then the non-superimposable, mirror image of the compound is the enantiomer.
  2. In order to have diastereomers, you need more than one stereocenter.  Sugars (saccharides) are the best example of this.  Look at glucose, it has 4 stereocenters.  The mirror image is the exact opposite configuration, so there is only one enanantiomer for glucose, but there are 7 diastereomers!
  3. Use the chart above to help you with R & S nomenclature and how that relates to enantiomers and diastereomers, this is how you will frequently encounter them after the first exam.
  4. Look for planes of symmetry to identify meso compounds.

How to Ace Orgo II — Five simple things you should know when taking Orgo II

Posted on January 16th, 2017

Welcome back!

Whether you were on vacation or just getting back into the swing of things– many of our students are beginning or will just be starting their coursework in the second semester of organic chemistry –known as Orgo II

Orgo II, or O-Chem II is a challenging course, but it doesn’t have to take over your life. Orgo I is typically harder, because many students are getting used the language of organic chemistry. But Orgo I and Orgo II are usually rather different and here is why:

  1. Orgo I focuses much more on concepts rather than memorization, while Orgo II requires more memorization– There are certain concepts that are covered in Orgo I that must be understood before learning the various organic chemistry reactions. Once that is complete, you can move on to learning the reactions and understanding what you are studying. If you are comfortable with that you will notice that Orgo II involves learning many more reactions, much more quickly than in the first semester
  2. Orgo II requires that you build on your knowledge of Orgo I — Organic chemistry is cumulative. Meaning that what you learned in Orgo I you must know in Orgo II. So if you need a refresher on Orgo I material, I suggest you do so prior to delving into Orgo II. Our Summary Guide and Exercise Sets are a perfect way to brush up on your Orgo I basics. covers these beginning topics in a simple and easy to understand format. Many of them are available free of charge!
    1. Introduction to Organic Chemistry
    2. Drawing in Organic Chemistry
    3. Molecular Orbitals, Hybridization and Geometry
    4. Lewis Structures, Formal Charge and Resonance Structures
    5. Basic Naming in Organic Chemistry- Naming Alkanes
    6. Organic Chemistry Functional Groups
    7. Acid-Base Chemistry
    8. Isomers
    9. Stereochemistry, Chirality and Enantiomers
    10. Introduction to the Study of Organic Chemistry Reactions
  3. Orgo II requires that the student be diligent and organized. As you learn the various reactions you will soon see that there is a lot to keep track of for each reaction. We suggest you be organized and disciplined and study a little each day. Take a look at how we organize our reactions— we suggest you do the same when you study and reference our material.
  4. As you study, be sure to establish connections in your mind on how the different reactions are related to one another. It is important to understand how you transition from one compound to another. This is especially useful in multi-step synthesis problems on your exams. For example, take a look at how we have organized the Orgo I reactions in our infamous Reaction Roadmap!
  5. Orgo II is your opportunity to soar in your organic chemistry studies. If Orgo I did not go so well or you struggled a bit- you are NOT alone! This is your opportunity to prove your organic chemistry skills. Many graduate school admissions committees specifically look at your grades in organic chemistry as it is known to be a challenging course. Aside from the actual grades in these courses, they will look at the trend- for example- did your grade improve from Orgo I to Orgo II? Maybe you got a B in Orgo I then got an A in Orgo II? That significant improvement from the first semester to the second semester speaks volumes to the potential of the student and is a great sign. So if you didn’t do as well as you wanted in Orgo I- don’t loose hope! A good grade in Orgo II can make all the difference!

Our team at is aware of these nuances and we are here to help you a long the way. Sign-up and join today! You can even take our tools on the go with our mobile app!

Happy Studying,


Chief Educator

Learning Reactions FAST!

Posted on October 26th, 2016


Learning organic chemistry is a very challenging for any undergraduate student, however it is a prerequisite course to many advanced degrees and necessary first step to understanding the reasons for how disease originates and how pharmaceuticals are designed to alleviate symptoms and cure disease.

One of the questions we receive at StudyOrgo frequently is “how do I learn reactions fast?”  The answer is different for each student and will require a lot of practice and patience on each student’s part, but we here at StudyOrgo have devised clear-cut and refined illustrations of over 180 examples of reactions commonly covered in the two semesters of organic chemistry.

To help you study gear up for your Fall Semester studying, we have outlined here some tips for studying organic chemistry reaction mechanisms quickly and efficiently.

Learn the basics of each reaction class mechanism: In this class, you will learn that the “flow of electrons” drives the mechanisms for every organic chemistry reaction. Understanding how electrons flow using specific functional groups is essentially all you are learning in this class!  Take for instance reactions of ketones.  Nucleophilic attack by hydride (H-) on the ketone carbonyl to form an alcohol uses the same mechanism as nucleophilic attack by H2O to form a diol, however the products are different because of the characteristics of the reagents.


Assemble a “road map” of reactions in the same class: Once you learn how electrons “flow”, all you need to do is memorize the reagents and what the produce! Tables work for some students, however StudyOrgo has come up with an interactive “Reaction Road Map” to help you trace what functional groups are interchangeable by using specific reagents.  This can greatly speed up your memorization of organic chemistry reactions!


Quiz you self with as many homework and sample problems as possible. StudyOrgo as developed a comprehensive set of over 180 reactions you will see in organic chemistry 1 and 2. We devised an innovative approach to integrate our extensive website content into the ability to aid fast studying of mechanisms into a Study Mode and Quiz Mode.

In Study Mode, all of the information is presented to you in a clear-cut format.  Reagents and products are presented the the left and right of the arrow.  Above the arrow, reagent that are necessary for the reaction are presented.  Below, Benny’s notes are listed to give you the tips and tricks of every reaction presented!  Very handy for learning the difficult or complex mechanisms!  Finally, the complete step-by-step mechanims with arrows, intermediates and transition states are depicted.  Several examples of each reaction are also illustrated in the website.  Use Study Mode to help you master these reactions fast, without paging through you notes or the book!


In Quiz Mode, you have the option to select any functional groups and add them to your custom quiz.  You can decide if you want reactants, reagents and products all covered up or just certain parts.  You can even select them to be randomized or in order, you can also choose how many questions you want asked!  Then save the quiz and take it!

You will see reagents and products are “covered up” to aid you in flash-card style studying of the material.  The “scratch pad” below the question will be useful for predicting what the answers will be. You can customize the Quiz Mode to cover some part or all parts of the reaction based on what you would like to quiz yourself on.  For example, if you professor says you are responsible for the reagents but not the mechanism, select reagents in Quiz Mode and only reagents will be hidden. This will help you to identify a reagent functional group transformation based on reagent choice.



Study every chance you get. StudyOrgo has developed an iOS and Android compatible app to help you with your studying needs!  With you membership, all reaction and website content is accebile to you anytime, anywhere!  Even use Study Mode and Quiz Mode with the app!


These are a few suggestions to making organic reaction memorization and as quick and painless as possible!  Sign up today to give it a try!

Intermolecular Forces Review

Posted on September 5th, 2016

Studying ahead for Organic Chemistry this Fall semester is a good way for reaching and maintaining a great grade in this class.  Most students find the pace of this class very challenging compared to other courses.  This is because while there is a lot of information to learn, it also builds on previous concepts from general chemistry, a course most students want to forget!

But don’t worry!  StudyOrgo has you covered.  Our Editors have spent years tutoring and teaching Organic Chemistry to students and we have seen all of the pitfalls common to the first few weeks of the semester.  Our online platform allows members to learn organic chemistry concepts and mechanisms quickly and the material presented in an easy-to-follow format. Follow along with us and sign up with StudyOrgo today to help prepare you for all of your Organic Chemistry questions.

One of the concepts you will need to have mastered before you  begin the class is Intermolecular Forces.

Permanent covalent bonds hold atoms together by electrostatic interactions between atoms. But these bonds can be very different. As such, molecules are held together by electrostatic forces between the molecules built upon the type of covalent and ionic bonds in the molecule.  These interactions have been characterized on the electronegativity difference between the types of atoms in the molecule and are classified as three different types

  1. Dipole-Dipole Interactions

These intermolecular forces are the result of electronegativity differences between the atoms that result in the amount of net electron density around each atomic bond.  In order to talk about these forces, a few definitions are necessary.  Let’s take acetic acid as an example.  It has one C-O bond and one C=O bond.  The result of the electronegativity difference is that the amount of electron density on carbon is reduced significantly as a result of the C-O bonds.  This leads to an overall reduction in electron density on carbon, a delta positive charge (blue color of orbital), and a gain of electron density on the oxygens, a delta negative charge (red color of orbital).  There is no real “charge” but the probability of electron density is higher around the oxygens, making them appear to have extra electrons, like an anion would have.  The “flow” of this electron density results in the formation of a dipole, which makes up a polar covalent bond.

figure 1

Polar covalent bonds will interact with each other (red dipoles) in the “like-dissolves-like” concept you learned in organic chemistry.  The dipoles will interact with each other, the delta positive of one molecule will interact with the delta-negative of another molecule to create a dipole interation.

figure 2

  1. Hydrogen Bonds

When there is a hydrogen atom bonded to an element with lone pairs of electrons, it is possible for the delta positive hydrogen (the hydrogen bond donor) of one molecule to interact with the lone pair of electrons on another molecule (the hydrogen bond acceptor).

figure 2

This can happen for any molecules in solution, therefore protic solvents (such as ethanol) can form hydrogen bonds with itself while aprotic solvents (such as methylether) cannot. The result is easily seen in boiling point, which is 78C for ethanol but -23C for methylether.  One rule is that hydrogen bonds must be planar to the hydrogen donor an acceptor, so there are some constraints on structure.  This is what gives DNA its helical shape, which you will encounter in another course.

figure 5

  1. London-Dispersion Forces

These obscure forces are best described as very weak, very temporary dipole moments between non-polar covalent bonds.  Let’s look at butane, an alkane.  There is a temporary flow of electrons between each C-C bond and for an instant, a net dipole between each C-C bond.  This allows for temporary interaction with a neighbor molecule that has the opposite temporary dipole, and so on.  The effect is thousands of weak dipole interactions that add up to a large force, and the basis for what we refer to as hydrophobic interactions.

figure 4