Archive for the "Organic Chemistry General" Category

Preparing for Organic Chemistry This Fall

Posted on August 5th, 2017

One of the questions we are repeatedly asked at StudyOrgo is “how do I to get ahead in organic chemistry this fall semester?” Many of you have heard that organic chemistry is a brutal class that does little but to depress your GPA. While it is true that this course is challenging, we here at StudyOrgo are devoted to helping you get the “A” you deserve!

Organic chemistry gets a bad name because it assumes that you are experts with regards to all of the general chemistry from freshman year, and you are now responsible to know it!  As an analogy, think of your chemistry courses as a pyramid to reaching your degree goals.  Organic chemistry is directly placed in the middle of the pyramid, it will be very important not only for the MCAT or DAT exams, but also for future advanced courses.  Organic chemistry is supported by General Chemistry, which is why you took it last year.  Fortunately, StudyOrgo is placed in the center of your pyramid base and we are here to help all of your organic chemistry questions.  Our simple and clear-cut explanations of reaction mechanisms and concepts will easily help you with anything you might struggle with this semester.  Here are a few tips on how to prepare today for the course this Fall.

chemistry pyramid

  • 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 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 on while studying over the 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. Think of it as a doctor or dentist 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.
  • Read ahead – If you have time this summer, read at least two chapters to get yourself ahead of the class. Don’t try to understand everything, just pay attention to the words used and the ideas. This will allow you to pay more attention and ask questions about the details in class instead of scrambling to write down notes and drawings.
  • Sign up with StudyOrgo – 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 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 help from StudyOrgo, you will have no trouble getting an “A” in Organic Chemistry this year!

In the reaction with ammonia, why is water the acid?

Posted on April 24th, 2017

In the reaction with ammonia, why is water the acid?

 

This is a great general chemistry reaction with important organic chemistry implications.  Another similar question is, why is water a base when reacted with an “acid”?  The answer to both question is: it’s all relative!  Here at StudyOrgo, we frequently get questions like this 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. With a membership to StudyOrgo, you will get even more tips and tricks on organic chemistry topics and detailed mechanisms with explanations.  Today’s blog is a preview of the detailed topics and materials available.  Check out a membership to StudyOrgo.com and sign up today!

 

Remember that in terms of acids and bases, there are two definitions; the Bronsted and Lewis definition.  Bronsted acids are defined as proton donors, while Lewis acids are defined as electron acceptors.  Both are acids, but what we think of differently is whether protons or electrons are involved.  In an aqueous solution, general chemistry or biochemistry, we mainly think of the Bronsted definition because the dissociation of protons from acids changes the solution concentration of H+, which we interpret as a change in pH and the “acidity” of the solution.  We measure the dissociation of the protons from acids, or the acceptance of protons by bases, with a numerical value which is the pKa.  The greater the pKa, the weaker the acid and stronger the base.  The lower the pKa, the stronger the acid and weaker the base. An easy trick for thinking of pKa is, place the protonated version of the molecule on the left and think of it as a proton donor.  The pKa tells you how easy this donation will be, the lower the number the easier the proton donation.

Let’s look at the ammonia and water reaction; the pKa for water is defined as 14.  The pKa for ammonia is ~37.

Therefore, because the pKa of water is lower than ammonia, it is a stronger acid the ammonia and will donate protons to the ammonia base.  This reaction leads water to become the conjugate base OH- and ammonia to become the conjugate acid NH4+.  Interestingly, this is why ammonia is a caustic agent, it produces hydroxide that reacts with stains and microorganisms to effectively clean and sanitize household items.

 

This is important as an organic chemistry concept because the strength of acids and bases in terms of electrons, or the Lewis definition, is exactly how we think about mechanisms of bond breaking and bond forming; the flow of electrons.  The strength of Lewis acids and the conjugated acid can help identify which direction a reaction will proceed.  We can see that the reaction of water an ammonia is unfavorable, but enough of the reaction occurs in reality to significantly reduce the pH of water (pH~11 with ammonia).

Let’s look at an acetylene reacting with a base to generate an alkynide ion, a useful nucleophile for C-C bond formation.  If we try to react sodium hydroxide with alkyne, alkynide ion WILL NOT be formed.  This is because the conjugate acid product of the reaction is water, which has a pKa of 15, is STRONGER than the original acid acetylene (pKa = 25).  Reactions ALWAYS favor formation of the weaker acid, or in this case, the reactant side.

If we change our base to sodium amide, which is a much stronger base, alkynide ion WILL be formed.  This is because the conjugate acid product of the reaction is ammonia, which has a pKa of 38, and is a WEAKER conjugate acid than the original acid acetylene (pKa = 25).  In this case, the reaction favors the product side!

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 StudyOrgo.com.  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 StudyOrgo.com.  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

cloro

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.

Screen Shot 2014-12-18 at 1.00.28 PM

Screen Shot 2014-12-18 at 1.00.18 PM

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.

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

Happy Studying,

Daniel

Chief Educator

StudyOrgo.com