Archive for the "Q and A" Category

Chirality and Assigning Stereochemistry to Molecules

Posted on August 11th, 2015

One of the most important skills to master in organic chemistry is the ability to assign stereochemistry.  We at StudyOrgo have devised clear cut explanations of these difficult concepts for students to maximize their time studying and learn difficult concepts quickly and easily. Sign up with StudyOrgo.com today for all of your organic chemistry studying needs!

Chirality is an important aspect of life.  This is so because many of the basic molecules used in living cells, in particular amino acids that form enzymes, are also chiral. Chirality imparts asymmetry on our molecules, allowing them the ability to recognize “handedness” and further add to the complexity and specificity of reactions. As organic chemists, we must pay constant attention to the chirality of molecules both before and after reactions, less the compounds lose their biological or chemical activity.

Chirality is defined as any object in which the mirror images are not superimposable. A good example is your hands; they are mirror images but not superimposable. Translating this to organic molecules, a stereocenter is a carbon center with 4 unique substituents that are arranged such that the mirror image is not superimposable. Thus, they “look” like to different molecules although they have the same substituents. If we alter the arrangement of the substituents, we can always come up with 2 arrangements for each substituent, R or S configuration.  Thus, each stereocenter must have 2 stereoisomers.

chiral 1

In order to determine whether the sterecenter is the the R or S configuration, there are a series of steps to follow.

  1. Identify the stereocenter as 4 unique substituents attached to the chiral center
  2. Assign priority based on atom atomic number, highest (1) to lowest (4) weight.
  3. If two atoms are same, move to next bond to find first point of difference
  4. Rotate the molecule so that Priority 4 atom is in the hashed wedge position.
  5. Determine the Priority sequence 1-2-3 rotates to the left (S) or the right (R).

chiral 2

Lastly, an important concept to keep in mind is that as molecules become more complex, they also can acquire more stereocenters.  Keeping in mind that each stereocenter can produce 2 stereoisomers, we describe possible stereoisomerism using the 2n rule. Let’s examine a molecule with 2 stereocenters, following the 2n rule that gives us 22=4 stereocenters.  The possible combinations are listed below.

Screen Shot 2014-12-18 at 1.00.28 PM

We now introduce the last concept to stereochemistry which is the difference between enantiomers and diastereomers.  Enantiomers are molecules with exactly opposite stereoisomers.  For example, the enantiomer of the molecule with stereochemistry R,R would be S,S.  The relationship between molecule R,R and R,S is what is described as diastereomers, which differ in some but not all stereocenters.

Let’s consider the biologically active form of testosterone, 5-DHT which is shown below.  We indicate that it has 7 stereocenters in the molecule.  Applying the 2n rule, we calculate 128 possible stereoisomer combinations.  That concludes that while testosterone has 1 enantiomer, it has 126 diastereomers and remember…only 5-DHT works on our bodies!

Screen Shot 2014-12-18 at 1.02.36 PM

 

Acids in Organic Chemistry

Posted on July 20th, 2015

Key Concept #1: Identify the Bronsted Acids:  The first concept we have to keep in mind is there are two kinds of molecules, proton acceptors and proton donors.  Acids are considered proton donors. That means they have to give up a proton to another molecule.  Bases are therefore proton acceptors, meaning they have to accept a proton from another molecule, this requires at least a lone pair of electrons and usually a negative charge on the atom.

acids 1

Let’s look at the reaction above.  If we dissolve HCl gas into water, then the water becomes the Bronsted base because it accept the proton from HCl.  Since HCl is a strong acid, we know that this reaction far to the right.

Key Concept #2 – Determine [H3O+] in solution to measure acidity: As we dissolve Bronsted acids and bases into solution, the concentration of H3O+ in solution will change.  Remember though, that concentrations are in units of moles (M) and have a wide range of concentrations in solution (typically 10+1 to 10-15 M).  Since it is clumsy to use such large numbers, we transform this concentration into powers (the p in pH) of the concentration of H3O+ (the H in pH) in the equation below.

pH=-log[H3O+]

Now, let’s take a look the pH of some household items to relate what pH really means.  Milk has a pH of 6.7.  If we solve for [H3O+] in the equation above, we find this is 2×10-7M or 0.2mM.  This is very similar to water (pH=7) which is 1×10-7M or 0.1mM, so not very acidic.  Coca-Colaâ has a pH of 2.5, solving for [H3O+] we find the concentration of proton is 3.1×10-3M or 3,100.2mM or more appropriately denoted 3.1mM.  This tells us there is 15,000 times more acid in cola than milk or water.  So, it is important to keep in mind the change of pH by 1 unit equals 10-fold change in [H3O+].  There are even more dramatic changes in pH between household items that can help you to appreciate the relationship between pH and [H3O+] in the chart below.

acids 2

Key Concept #3 – Predicting the equilibrium of the reaction:  The numerical value associated with acidity is known as pKa, which is the equilibrium concentration of the acid and conjugate base. The higher the value, the more acidic the solution.  There are two key tips in predicting acidity; 1) equilibrium lies towards the weaker acid (a low pKa towards a higher pKa) and 2) equilibrium lies towards the most stable conjugate base.

Lets take a look at the following reaction.  If we know the pKa values of the acid and conjugate acid, we can easily see that acetic acid (pKa = 4.75) reacted with sodium hydroxide produces the conjugate acid water (pKa = 15.7).  Equilibrium will therefore shift to the right.

acids 3.jpg

Many times, however, you do not know the pKa value of the acid or the conjugate base.  Therefore we can predict equilibrium based on the stability of the conjugate base based on the follow four rules;

There are four factors to consider when comparing the stability of conjugate bases:

  1. Atom which has the charge—For elements in the same row of the periodic table, electronegativity is the dominant effect. For elements in the same column, size is the dominant effect.
  2. Resonance—a negative charge is stabilized by resonance.
  3. Induction—electron-withdrawing groups, such as halogens, stabilize a nearby negative charge via induction.
  4. Orbital—a negative charge in a sp-hybridized orbital will be closer to the nucleus and more stable than a negative charge in an sp3-hybridized orbital.

Below in the example, penanedione is reacted with sodium azide to make a enolate anion.  If we didn’t know the pKa of the acids, we could examine the base stability to determine equilibrium.  The azide anion as a negative charge on nitrogen and is somewhat stable. Although the negative charge on the conjugate base is carbon, which is less ideal than nitrogen, it has two neighboring carbonyls that contribute stability from resonance, inductive forces and the
sp-2 hybridization of the conjugate base.  For these reasons, we would predict the equilibrium to the right.  We in fact are correct since pKa of the acid, pentanedione, is 9 and the conjugate acid, ammonia, is 38.  Therefore, this reaction is 10^29 fold (i.e. pKa 38 – pKa 9) towards the right!

acids 4

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Naming Organic Molecules

Posted on June 18th, 2015

Naming molecules is a challenging exercise because there are many rules; the more complex the molecule, the more rules that need to be observed.  It is possible to name a single molecule in many different ways, but only one is correct!  These are easy points on quizzes and exams and can boost your grade if you know how to tackle them. We here at StudyOrgo have summarized the process down to 4 easy steps to name alkanes.  Follow along to determine the name of any molecule in your course.

Four discrete steps are required when assigning the name of an alkane:

  1. Identify the parent chain: Choose the longest chain. Looking at the first example below, several chain lengths are shown, however only the red trace contains the longest chain, therefore this is the correct parent chain. For two chains of equal length, the parent chain should be the chain with the greater number of substituents. In the second example below, two 7-carbon chains are possible, but only one gives 2 substituents, so it is therefore the correct parent chain!
    nomenclature 1
  2. Name the parent chain: In order to correctly name the parent chain, you will have to commit to memorizing the prefixes that denote how many carbons are in the parent chain. There is no easy way around it, so try covering the table up and recalling to help with memorization.
Number Of Carbons Parent Name AlkaneExample Number Of Carbons Parent Name AlkaneExample
1 meth methane 11 undec undecane
2 eth ethane 12 dodec dodecane
3 prop propane 13 tridec tridecane
4 but butane 14 tetradec tetradecane
5 pent pentane 15 pentadec pentadecane
6 hex hexane 20 eicos eicosane
7 hept heptane 30 triacont triacontane
8 oct octane 40 tetracont tetracontane
9 non nonane 50 pentacont pentacontane
10 dec decane 100 hect hectane

 

  1. Number the parent chain, identify and assign a location (carbon number) to each substituent: Just as with the parent chain prefixes, substituent prefixes are another terminology you will have t memorize! Give the first substituent the lower possible number. If there is a tie, choose the chain in which the second substituent has the lower number.  In the example of methyloctane, the methyl position could be at position 2 or 7. The lowest number prevails so 2-methyloctane is correct.
    nomenclature 2
Number Of Carbons In Substituent Terminology
1 Methyl
2 Ethyl
3 Propyl
4 Butyl
5 Pentyl
6 Hexyl
7 Heptyl
8 Octyl
9 Nonyl
10 Decyl
  1. Arrange the substituents alphabetically: Place the number corresponding to the position in front of each substituent. Note for the example below, there are four identical ethyl substituents, therefore we will label each position followed with the prefix tetra (di- for 2, tri- for 3, etc.) Note, the prefix is NOT included in alphabetization, as methyl comes after ethyl regardless of the “tetra” prefix in this example.
    nomenclature 3

And there you have it. With a little practice and help from StudyOrgo, you are well on your way to naming any organic molecule in your studies.  Sign up today for help with terminology, reaction mechanisms and more!

How To Get Ahead For The Upcoming Semester

Posted on January 13th, 2015

Use your iPad or iPhone to study on the go during your break.

Use your iPad or iPhone to study on the go during your break.

One of the questions we receive here at StudyOrgo frequently is how to get ahead for the next semester. Arguably, the second semester of organic chemistry is much more challenging for students than the first. This is because all of the general chemistry refresher and organic chemistry introductory material has been covered and you are now responsible for it! You may have covered addition reactions, maybe substitution and elimination if your professor was on task. But that covers the reactivity of only 3 of the more than 20 functional groups you will study in this class! Thus, the speed of the course is about to pick up. We have developed a few helpful hints to take advantage of your winter break and get ready for the spring semester of organic chemistry.

  • Open your text book – Shockingly simple, often overlooked. Simply 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 – Organic Chemistry II is often a continuation of Organic Chemistry I and likely you will have the same professor or pool of professors from the first semester. 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 semester.
  • Schedule your studying NOW! – 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 a week or two left, read at least two chapters over the break once through 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 StudyOrgo, you will have no trouble getting an A in Organic Chemistry this year!

Preparing to Study Organic Chemistry

Posted on August 28th, 2014

Many students find themselves lost by the end of semester in Organic Chemistry.  This has led to a terrifying perception of Organic Chemistry that is passed down from upperclassmen.  We at StudyOrgo are here to say, you can make it!  You just need the right strategy to succeed.

“Divide and Conquer”

247The best way to stay ahead of the semester is to divide your chapters into blocks that you will study.  Most professors will have a fairly clear outline of what chapters from your book will be covered before each exam.  Your goal here should be to divide your time (starting right now!) until the exam into blocks to study.  Some chapters, like substitution (e.g. SN2) and elimination (e.g. E2), are longer than others because these reactions are the foundations for future reactions you will learn later in the course.  So, spend a lot of time mastering these important topics.  Finished a chapter early?  Move ahead and don’t wait until you receive the lecture to start studying.  Many people find studying before the lecture help them to really understand what the professor is saying and will give you an opportunity to ask questions right away.

But remember; no one is a better judge of your understanding than you!  If any material is unclear, don’t move forward until you are confident and seek help immediately.  StudyOrgo.com has developed a customized presentation of difficult concepts in organic chemistry into an easy to understand format with a step-by-step breakdown and description of common reaction mechanisms in organic chemistry.

 Schedule your studying times

To achieve your “divide and conquer” plan, get serious about studying the material.  The best way to this is to schedule yourself an “appointment.”  Carry out your studying at a designated spot, we recommend not studying in the comfort of your home or dorm room where distractions are copious.  Pick a coffee shop, library or classroom to force yourself into studying.  Learning these time management skills will not only help you earn a passing grade in Orgo, it will help you in your career as well!

Practice Problems

Professors are notorious for advertising to their students that homework is not mandatory and/or you will be graded on the homework.  Relax then, right?  Wrong!  An important realization to make is that there are only so many types of questions a professor can ask.  Therefore, if you see a ton of practice problems, chances will be high you have already seen the exam problem. Many professors will throw in “really hard” questions that terrify students and it may seem like they are just being plain evil.  There is a reason for everything!  Professors use this tactic to assign A’s to the students who have kept up and followed along the whole time and rightfully so since these questions cannot be answered without understanding everything they have covered.  You can be one of the few who aces these questions!

Review Materials before the Exam

Either you have been following the steps above the whole semester and you are ready for that exam… or you read our article too late and the exam is next week.  There is still hope!  Simply adjust the “divide and conquer” strategy to fit the time you have remaining until the exam.  We suggest you review ALL of the material though and not just what you think you don’t know.  In our experience, the difficulties students have are often because they missed a concept earlier on.  Orgo is like a pyramid, the top falls without a strong base.  Here at StudyOrgo, we have developed easy to follow review study guides and exercise sets to help with reviewing all the concepts you will have to master to pass the course!  Check out www.studyorgo.com/summary.php for more details!