Archive for the "Organic Chemistry General" Category

Students often mention to us they are confused about the rules of aromaticity and how best to study for difficult examples.  We at StudyOrgo.com have developed a clear and “get-to-the-point” presentation of the basics of aromaticity.  This is just a sample of the clear-cut explanations available on our website to our members.

Aromatic Compounds

Aromatic compounds are unusually STABLE and have important chemical and synthetic uses.  In fact, nucleic acids and amino acids that make up every cell rely heavily on the use aromatic compounds.  But, what makes a compound aromatic?  A short list of rules, discovered by Eric Huckel in the 1930’s, lists the properties of aromatic compounds.

The Huckel aromaticity rules are:

1. Molecule is cyclic
2. Have one p orbial per atom of the ring
3. Be planar, in an sp2 hybridized orbital, over every atom of the ring
4. Have a closed loop of 4n+2 pi-bond electrons, where n is equal to any integer (0,1,2,3,…)

But like most natural phenomenon, there exists a rule exactly the opposite.  Molecules that have an unusual INSTABILITY to them are anti-aromatic compounds.  They have similar rules to aromaticity, including:

1. Molecule is cyclic
2. Have one p orbial per atom of the ring
3. Be planar, in an sp2 hybridized orbital, over every atom of the ring
4. But, anti-aromatic compounds have a closed loop of 4n pi-bond electrons.

Below are the pi-orbital diagrams of benzene, the most identifiable aromatic compound.  Each of the three double bonds contributes 2 pi-electrons over 6 atoms, for a total of 4*1+2=6 electrons, in a ring, in a pi-orbital that is planar.  Therefore it is aromatic.  In contrast, hexatriene meets all of these criteria as well, but is not in a closed ring.  Hexatriene is therefore non-aromatic.  Finally, cyclobutadiene is the most identifiable anti-aromatic compound which is different only in that it has 4*1=4 pi-electrons, in a ring, in a pi-orbital that is planar.

Heterocyclic Aromatic Compounds

The diversity of compounds relies on using atoms other than carbon, however.  What about when atoms with lone pairs of electrons are involved?  A good rule of thumb is that if the atom is already participating in the pi-bond forming in the ring, then the lone pair of electrons are perpendicular to the ring and therefore are NOT participating to aromaticity.  A good example of this is pyrimidine, where both nitrogens are already contributing to the pi-bond ring and therefore, the lone pairs of electrons are not accessible.

However, there are many molecules where lone pair DO participate to aromaticity.  Below are several examples.  Take furan for example; oxygen has two lone pairs of electrons.  One of them is in a geometry parallel to the pi-bond system.  Therefore, these electrons DO participate in the pi-bond system and add 2 electrons the pi-bond count resulting in 4*1+2=6 electrons, therefore furan is aromatic.  Imidiazole is molecule that has two nitrogen atoms; one nitrogen participating in pi-bonding and not contributing lone pairs, while the other is not participating in pi-bonding but contributes electrons the pi-bond count.  The 4*1+2=6 electron count for imidazole renders it aromatic.

Aromatic Hydrocarbon Ions

Sometimes, carbocations and carbanions are produced in chemical reactions.  If these species are created in a cyclic conjugated system, it is possible that they can contribute to the formation of a Huckel aromatic compound, which gives the molecule added stability and special reactivity.
For example, cyclopentadiene is not aromatic because of the sp3 hybridized carbon at position 5 on the ring.  However, in the presence of strong base, cyclopentadiene can be deprotonated and cyclopentadienyl anion is generated.  The lone pair of electrons assumes a sp2 hybridized orbital, making the molecule planar, adding 2 more electrons to the ring to give 4n+2 pi-electrons and creating the 5th pi orbital necessary to complete Huckel’s Rule and results in an aromatic ion.

Another example is formation of a carbocation, a common intermediate in substitution and elimination reactions.  Deprotonation of cycloheptatriene, a non-aromatic compound, at the sp3 hybridized position creates a sp2 hybridized orbital and, although this carbon’s pi-bond orbital is empty (a carbocation), it completes the 7th pi orbital necessary to complete the ring and maintains a 4n+2 electron count.  This carbocation, called tropylium ion, is now aromatic.

This is a problem that plagues many students studying organic chemistry and it is one of the cornerstones of getting through the class.  Without a clear understanding of stereochemistry, determining the correct product for future reactions will be impossible, so let’s break it down into some simple concepts.

• Concept 1 – in order to have stereoisomers, the molecule must be CHIRAL.
  • Remember in order to have chirality, molecules must have the following characteristics
    • Carbon center with 4 unique substituents, meaning they are chemically distinguishable from each other.
      

• In this example, the molecule on the left has 3 red hydrogens.  These hydrogens are chemically indistinguishable from each other.  So the molecule is ACHIRAL.
• The molecule on the right has 1 red hydrogen and 3 other unique substituents.  Therefore, the molecule is CHIRAL.
• Concept 2 – Chrial molecules that have STEREOISOMERS.
  • Stereoisomers are molecules that have the same chemical formula, but differ in their arrangement at a chiral center.
    

• Concept 3 – Stereoisomers are identified by their “HANDEDNESS”, which refers to the arrangement of the substituents relative to their importance.
  • In general, elements of higher mass have higher priority.  Refer to our tutorial on chirality for more details.
    

• Concept 4 – There are two types of STEREOISOMERS, enantiomers and diastereomers.
  • Enantiomers contain chiral centers that are non-superimposable & mirror images.  They only come in pairs!
  • Diastereomers contain chiral centers are non-superimposable but are NOT mirror images.  There can be many more than 2 depending on the number of stereocenters.

An easy way to remember enantiomers from diastereomers is to memorize the picture below.  In the case of 2 chiral centers, 4 stereoisomers are possible.  Only the exact opposites (diagonal arrows) are enantiomers and they therefore have a mirror image that is not superimposable.  The molecules with only one stereocenter that differs (parallel arrows) are diastereomers.  

A biological example of this is saccharide (or sugar) chemistry and below is the enantiomers and diastereomers of threose.

While enantiomers can only come in pairs, many diastereomers can exist for a given molecule.  Let’s take, 5-DHT for example, the metabolically active form of testosterone.  This molecule has 7 stereocenters, using the 2^N rule for determining the number of stereoisomers, which gives 128 possible combinations. But only one of them is the enantiomer of 5DHT!  The rest are diastereomers.

This is just an example of the crystal-clear explanations you will receive as a member of StudyOrgo.com about important, and often confusing and poorly explained, concepts in organic chemistry. Our site developers have listened to students’ concerns and have come up with clear visuals to our tutorials on organic chemistry topics.  Interested further?  Sign up today!

“I have an exam next week and I feel helpless right now. I feel like I do not understand anything at this point meanwhile I have had a good understanding for the past two exams. Will this site be beneficial to me since I have a short period of time to my exam?”

We receive comments like this frequently at StudyOrgo. To summarize the student’s dilemma, it sounds like the first two tests worth of material in organic chemistry were the basics: learning to name compounds, bond hybridization, sigma and pi bonding, maybe even some thermodynamics and bond energies. But now that you have covered these fundamental principles, it is time to put them into practice and learn about specific chemical reactions and their mechanisms. In this course thought, the quantity and variety of reactions can be just as overwhelming as their complexity. This is usually where it the course goes sideways for students, and a feeling of panic and despair replaces any confidence you felt about the material before.

When asked if this website will help a student in this predicament, our short answer is “YES!” What is likely this student’s trouble is either some important concepts critical to the new material were missed or not understood as well as previously thought. It happens all the time. Many times, students will tell us that the teacher “blew through” or “went really fast” over some material and the student missed it. After we re-learn the materials presented on the website, the student can be acing the practice problems!

What you need to move forward is to solidify the base of your pyramid of organic chemistry knowledge. You were off to a good start, but something went wrong somewhere, and we have the expertise to help. We at StudyOrgo have spent countless 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 get it based from the tutorials we present.

Once you are ready to move on past the basics, we take a step-by-step approach to going over every chemical reaction commonly taught in the course. We make a note to point out important points, Markonvnikov v. anti-Markovnikov selectivity, syn or anti addition, stepwise v. concerted mechanism, etc. By the time you finish the tutorial, you will be ready to practice you problem sets and you will be ready to ace the next test!

This is a common question from undergraduates seeking to satisfy requirements of medical school applications.  First, let’s start with some stats on getting into medical school.  The American Association of Medical Colleges reported that total students enrolled in medical school (over 4 classes of students) has risen from 77,353 in 2009 to 83,472 in 2013.  That’s good news, as this indicates that enrollment has risen by more than 7000 students, or roughly 1700 more slots for incoming classes.  This means that the chance of entering medical school is higher than it has ever been!  However in 2013, of the 20,055 students who matriculated into a medical school, 48,014 applicants applied with an average of 14 applications per applicant, for a grand total of 690,281 applications submitted and reviewed.  That translates to roughly a 40% acceptance rate.  This concludes getting into medical school is fiercely competitive which is why many student obsess about getting the best grade possible.

In an article from U.S. World News, Johns Hopkins premed advising office suggests that an applicant with a GPA of 3.5 and a MCAT of 30-31 stands a “good chance” of getting accepted, but factors such as personal statements, experience, community service, spoken languages and applicant interview also majorly impact your chances.  No doubt you must demonstrate a mastery of all of the subjects required for medical school applications, including organic chemistry, but clearly grades are not the only metric of acceptance.  Here are a couple of suggestions for maximizing your organic chemistry studying to get the edge on the competition.

• Don’t get caught up in counting points
  • Students often spend considerable time and energy complaining to teachers and graders over 1 or 2 points here and there.  This is penny-wise and dollar-foolish. A few points will have little to no impact on your grade.  The most important use of your time studying are the big pictures.  Understand where minor points were taken off and make efforts to avoid these simple mistakes in the future.  Keep calm and move on!
• Practice, practice, practice!
  • Professors have only an hour or two at most to examine your knowledge of weeks of material.  That means they have to ask you the major concepts in order to satisfy the curriculum and there are only so many types of questions they can ask.  Seeing as many practice problems as possible will give you a very good understanding of the big picture and ensure success on most of the test.  Sometimes, professors will throw in a “really hard” example.  These questions are meant to discriminate between the “A’s” and the “B’s.”   But, if you have practiced many problems, your chances for having seen these questions raise dramatically.  It’s a win-win to practice everything problem you can find!
• Get help from StudyOrgo 
  • Even the best organic chemistry student will struggle with a concept here and there.  Regardless of your past success in the course, outside tutoring will always help.  At StudyOrgo, we have developed intuitive and in-depth descriptions of most reactions in organic chemistry.  We take each mechanism step-by-step with many examples to show you how reactions proceed and point out how they can vary.  With hard work and assistance from StudyOrgo, you are sure to get the A you deserve and give you the extra edge when preparing for medical school!