How to Assign Stereoisomer Configuration

Posted on July 2nd, 2018

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

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Molecules, like your hands, that are not superimposable on their mirror images are called chiral objects, from the Greek word cheir  (meaning “hand”). All 3D objects can be categorized as either chiral or achiral. Chemical molecules are 3D objects and can also be classified in this way. To help you remember, chiral molecules are like hands and are NOT superimposable on its mirror image while achiral molecules are like tennis rackets: they are superimposable on their mirror images.

IUPAC recommended in 1996 that a tetrahedral carbon bearing four different groups be called a chirality center.  Many other names are commonly used include chiral center, stereocenter, stereogenic center, and asymmetric center.  They all mean the same thing, a carbon connected to 4 unique substituents that is not superimposable on its mirror image.

When a compound is chiral, it will have one opposite molecule; a non-superimposable mirror image, called its enantiomer (from the Greek word meaning “opposite”). The compound and its mirror image are said to be a pair of enantiomers. The word “enantiomer” is analogous to the word “twin”. When two children are identical twins, each one is said to be the (“evil…”) twin of the other. Similarly, when two compounds are a pair of enantiomers, each compound is said to be the enantiomer of the other.  A chiral compound will have exactly one enantiomers, all other molecules with the same molecular formula and constitutional arrangement are diastereomers, but are only seen when there are more than two chiral centers in a molecule.

In order to determine whether the stereocenter is in 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

  • This one is easy for most, but just look for any carbon with 4 substituents that are different.  Be careful to carefully count chain lengths and identify unique elements.

2. Assign priority

  • Step 1: Assign priority of bond based on atom atomic number of the element, highest (1) to lowest (4) weight.
  • Step 2: If two atoms are same, count the type of bonds connected to the carbon to find first point of difference
  • For 2-methyl-3-pantanol, oxygen is highest priority and hydrogen is lowest priority. However, 2 carbons are connected to the stereocenter, therefore count the number of bonds connected to each carbon center. In this case, the carbon with 2C and 1H has higher priority than the carbon with 1C and 2H.
  • For the haloalkane, oxygen is highest priority and hydrogen is lowest priority. However, 2 carbons are connected to the stereocenter, therefore count the number of bonds connected to each carbon center. In this case, the carbon with 1Br and 2C is higher priority than the carbon with 1F, 1Cl and 1C because Br is the heaviest and highest priority element.

 

3. Rotate the molecule so that Priority 4 atom is in the hashed wedge position.

  • In some cases, if you can’t flip the molecule in your head or on paper easily, assign the configuration to the stereocenter when the 4th position is NOT in the back of the paper position, and just reverse the assignment.  It works every time.

4. Determine the Priority sequence 1-2-3 rotates to the left (S) or the right (R).

 

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.

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.

Formation of Enols and Enolates

Posted on April 3rd, 2018

One question that comes up in organic chemistry often is “what is an enol or an enolate and how is it formed?”  These types of concepts are frequently covered quickly in class or not at all, but are very important for future reaction mechanisms.  We at Study Orgo have the combined experience of over 15 years of tutoring and teaching organic chemistry concepts to struggling students.  We have developed clear descriptions of reaction mechanisms and organic chemistry concepts to aid students in their studies.  Sign up today for access to over 180 reactions mechanisms and reviews!

The alpha carbon of a carbonyl, which is present in carboxylic acids, esters, ketones and aldehydes, are acidic which means the proton can be removed using a base.  In neutral or acidic conditions, this means the lone pairs on the C=O position can act as a weak nucleophile.

If the carbonyl oxygen can attack the alpha carbon C-H bond, it will abstract the hydrogen and perform a Keto-Enol tautomerization reaction that will lead to the resonance version of the carbonyl, which is the Enol (alkENE + alcohOL)

Enols – rearranging the pi bond and atoms of a carbonyl compound to an Enol

Catalyist: Acidic or Neutral Conditions to stabilize OH formation

Enols tautomers are generally unstable, preferring the “Keto” version 90-99% of the time versus the “Enol” version.  However, a catalytic amount of presence is sometimes enough to drive reactions forward if the mechanism requires the enol tautomer of the compound.

However, in some cases such as a beta diketone, shown below, the combined dipoles of two carbonyls makes the alpha carbon very acidic, meaning enol formation is very favorable.  In this case, it is 70-90% enol in solution.

 

Enolates – Deprotonating the alpha carbon and tautomerizing to the oxyanion

Catalyist: Strong Base to deprotonate the alpha carbon.

Like an Sn2 mechanism, a strong enough base will react with the acidic proton on the alpha carbon and deprotonate.  The electron density between the C-H bond will shift to make a new C=C bond, while the C=O electrons will be placed on the oxygen, creating and alkENE + alcohOL anion “ATE”) with a strong base to produce a stable carbanion.  The stability is due to the tautomerized structure that can be produced by placing the negative charge on the oxygen.

 

Enolates are generally forward reactions depending on the strength of the base.  How strong the base required depends on the pKa of the alpha C-H bond.  In the case of ketones, a strong base like LDA is required.  However, for beta dikeontes, a mild base like NaOH is enough to generate the enolate.

 

Formation of Enols and Enolates are an important source of carbon nucleophiles to make new C-C bonds in future reactions.

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How do you to tell when a hydrogen bond will occur?

Posted on March 7th, 2018

Hydrogen bonding is important for describing the driving force of reactions in organic chemistry and a very important concept for explaining the biochemistry of catalytic reactions that occur using protein as enzymes in biological systems.  In this post, we will discuss the rules and examples of hydrogen bond formation.  We at StudyOrgo have extensive experience instructing principles and reaction mechanisms frequently covered in Organic Chemistry. Sign up today for clear, detailed explanations of over 180 Orgo Chem reactions and reviews on conceptual topics!

Physical properties of molecules such as boiling and melting point, solubility and reactivity, are affected by the functional groups that make up the molecule. This can be explained by analyzing the type of intermolecular forces that are experienced between molecules.  Because these forces are not covalent, intermolecular forces are determined by the intensity of electrostatic forces which is what makes up each type of intermolecular force. As a review, the types of intermolecular forces are;

  • Van der Waals (London dispersion forces) – Weak, temporary dipole formed between hydrophobic C-H and C-C bonds.
  • Dipole-Dipole Interactions: – Strong, permanent dipole moments formed between atoms of functional groups containing bonds such as C=O, C=N, C-O, C-N, N-H and O-H bonds. The delta(-) side of one dipole is attracted to the delta(+) side of another molecule, forming a non-covalent electrostatic attraction.
  • Hydrogen Bonding: Sharing sharing of a hydrogen atom covalently attached to an electronegative element (typically O-H and N-H groups) between a lone pair of electrons on another electronegative element.

Two terms about hydrogen bonding that are key are;

  • The electronegative atom with the lone pair electrons is called the Hydrogen Bond Acceptor
  • The electronegative atom bonded to the hydrogen is called the Hydrogen Bond Donor
  • The Hydrogen Bond Donor must be aligned 180 degrees to the Hydrogen Bond Donor!

The more intermolecular forces the molecule has, the more energy will be required to disrupt these bonds when melting or boiling compounds, thus raising the observed temperatures from expected relative to their mass.  In addition, hydrogen bonds require polar bonds in the molecule and H-Bond Donor proton involved is protic (a donatable hydrogen atom). These are two terms that you will learn in the Sn1 mechanism.

Let’s look at ethanol as an example.  The hydrogen bonding occurs between the proton of one alcohol group and the oxygen lone pair electrons on another alcohol group.  This is a strong intermolecular force that holds the molecule in a complex 3D shape and makes it easier in reactions to attack the carbon connected to the O-H bond due to inductive effects, or the pulling of electrons away from the carbon.  Water is an extreme example, where all the atoms in the molecule participate in hydrogen bonding.  The oxygen lone pairs will accept a hydrogen from a neighboring molecule O-H.  Finally, acetic acid is another example.  Remember, that the H-Bond Acceptor can be any lone pairs, including those of C=O bonds.

 

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.

IR Spectroscopy Review

Posted on January 14th, 2018

Studying ahead for Organic Chemistry this Spring semester is a good way for getting the best grade this semester and keeping up with the rigorous course work in Orgo 2.  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 Orgo 1, a course most students want to forget!  In your time before classes begin, consider reading ahead or brushing up on some concepts that were covered late last semester to give you a boost right away.

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 quickly in Orgo 2 is the usefulness of Infrared (IR) Spectrometry.  In this article, we will break down the key concepts and give you all the info you need to master this technique quickly.

IR Spectroscopy Principles

A usefulness of using light for analysis is it is relatively non-destructive and cheap to produce.  We can see that there are many regions of electromagnetic radiation that we can use for molecular predictions.  For instance, long wavelengths like microwaves are used in NMR for determining atomic structure.  Longer wavelengths like IR and UV/Vis region are used for predicting functional groups and can help you identify unknown compounds.

Infrared radiation causes vibrating the bonds between atoms.  This is a similar principle to how heating up molecules works, and you may have heard of infrared imaging systems, which can measure the relative temperature of molecules.  This technology works on a similar principle to IR spectroscopy, but we use it in the lab to determine functional groups.

Higher energy regions of the IR spectrum (larger wavenumbers) will cause stretching of bonds where lower energy regions (smaller wavenumbers) will cause bending and twisting.  Thus, depending on the type of bond and the atoms involved in the bond, we can predict what they are based on which wavenumber region they absorb.

There are 3 pieces of information you can get from the IR spectrum of samples.

Signal Region

In the graph above, we can see the IR spectrum for isopropanol.  We see that the range of wavenumbers (inversely proportional to wavelength), there are multiple regions that are causing unqiue-looking signals.  The functional groups are alkane and alcohol.  Almost all your moleucles will have C-C and C-H bonds, so many o fhtese signals are not useful.  But an alcohol is unqiue, with a large peak at 3400.

Signal IntensitySome signals will be weak and some will be strong, as we see in the figure above.  This has to do with how efficiently the region is being absorbed by the molecule.  If it is a strong signal it should be consistent and easy to detect.  However some bonds are not as efficient.  With these signals, sometimes you miss them because they are too weak.  So if you think you may have a functional group but the peak is not there, remember it maybe “invisible” if it is a weak signal. 

Signal ShapeMost types of bonds will absorb in a very narrow region of the IR, giving the typical narrow signal shape. Only a few types of bonds will case large regions of the spectrum to absorb, causes a broad signal.  These always are functional groups that can undergo hydrogen bonding, such as O-H, N-H, C=O, etc.  Typcially OH and COOH functional groups are very broad, while carbonyls are amines are more broad than ususal.

Common signals used to predict functional groups

 

Analytical Chemistry – Infrared (IR) Spectroscopy

We have placed a typical carboxylic acid spectrum on top of this trend chart to help you learn the various signals that you will encounter.  Signals in the “fingerprint” region are useful for matching you unknown to a known standard, too usually too “noisey” to predict anything.  You can see that the broad OH peak at 3400 cm-1 and the C=O peak at 1710 cm-1 falls very neatly in the trend.

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Studying Tips for End of Semester and Winter Break

Posted on December 5th, 2017

Many students find themselves struggling by the end of semester in Orgo 1.  To make matters worse, you are now staring at a difficult class in Orgo 2 next semester. How can you possibly get ready for this difficult class?  We at StudyOrgo are here to say, you CAN make it!  But to do it efficiently, you will need the right tools to succeed.  With winter break approaching, take advantage of this time to get ahead NOW, and with StudyOrgo you can really accelerate your success next semester.

Patch up your understanding with StudyOrgo

The best way to stay ahead for next 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 foundations for future reactions you will learn later in Orgo 2.  So, spend a lot of time revisiting these important topics if you felt lost in Orgo 1.  Finished a chapter early?  Many people find studying before the lecture help them to “feel” they really understand what the professor is saying and gives you an opportunity to ask questions right away.  Don’t have a book, or your book is terrible???  Check out the over 180 reactions at StudyOrgo that are clearly organized and expained!

Schedule your studying times

To force yourself to get the studying done, get serious about it!  The best way to do this is to schedule your studying as 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 everywhere.  Choose 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 2, it will help you in your career as well!

Read one chapters of the book per day, and just read it.

When its winter break, it can be hard to get motivated.  If its the end of the semester, there doesnt feel like there is enough time!  In either case, we strongly suggest starting by just reading the chapter.  Don’t stop to define words or look up something, just read it!  Put it down for a day and then read it again tomorrow. This time, try to define terms you don’t understand by using our powerful platform of topics to help clarify common conceptual problems.  Then read it a third time, you should be feeling familiar with the topics now, and you are ready to start putting it to use in the practice problem set!  Can you draw the mechanism?  Can you identify the correct reagents?  Here are StudyOrgo, we present all of our mechanisms.  Use our flashcard method for Review Mode for learning or Quiz Mode to help drill yourself on the problems.

Organic Chemistry Quiz

Practice Problems

Professors famously tell their students homework is not mandatory and you will not be graded on the homework.  Relax then, right?  Wrong!  Its important to understand that there are only so many types of questions a professor can ask.  So, if you see a hundreds, and we mean hundreds, of practice problems, then chances are you have already seen the type of problems that will be on the test. Many professors will throw in “really hard” questions that terrify students and it may seem like they are being unfair.  There is a reason for everything!  Professors use this strategy 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!  We have comprehensive reviews of the mechanism, stereoselectivity, regioselectivity, reaction considerations and more!

Review Materials before the Exam

Either you have been following the steps above the whole semester and you are ready to prepare for Orgo 2 this winter break… or you read our article too late and the exam is next week.  There is still hope!  Simply adjust your 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 combined 30 years of experience!!!, the difficulties students have are often because they missed a concept earlier on.  Do you know all of these topics??  If not, use StudyOrgo to patch up your understanding, or to simply check yourself.  We’ll bet you’ll find something you didn’t know in one of these topics!

Organic Chemistry Help

Remember, Organic Chemistry is like a block in the pyramid to get to  your science or medical career goal. 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 help with core topics in Orgo 1 that you will need to succeed for next semester!