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.

This is just an example of the clear-cut description of Orgo 2 concepts that we explain at  Sign up to day to get ahead on over 175 reactions commonly covered in these classes!

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 for help with core topics in Orgo 1 that you will need to succeed for next semester!

What is the difference between Sn2 and Sn1?

Posted on October 20th, 2017


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!

Substitution reactions involve the attack by an electron-rich element, referred to as the nucleophile, on an electron-poor atom, referred to as the electrophile.  As the reaction name suggests, we are substituting the nucleophile for another group on the electrophile atom, which is referred to as the leaving group.  The generic reaction looks like this.

In Substitution reactions, there are two mechanisms that will be observed.  An Sn2 and Sn1 reaction mechanism.

Sn2 reactions are bimolecular in rate of reaction and have a concerted mechanism.  The process involves simultaneous bond formation by the nucleophile and bond cleavage by the leaving group.  The transition state looks like this.  Because the reaction is concerted, Sn2 mechanisms will always lead to an inversion of stereochemistry!  For reactivity using an Sn2 mechanism, primary >> secondary >> tertiary carbon centers.


On the other hand, Sn1 reactions are unimolecular in rate of reaction and have a step-wise mechanism.  This process first involves bond cleavage by the LG to generate a carbocation intermediate.  The stability of carbocation formation will determine if Sn1 or Sn2 reactions occur.  In the second step, the electronegative nucleophile attacks the carbocation to form the product.  The steps look like this. Because the nucleophile can attach either side of the carbocation, which adopts an sp2-hybridized orbital with a trigonal planar geometry, an equal amount of inversion and retention is seen, referred to as a racemic mixture. For reactivity using an Sn1 mechanism, tertiary >> secondary >>> primary carbon centers.

The strength of nucleophiles used help to determine the reaction mechanism.  Strong bases will almost always proceed to Sn2 mechanism.  Weak nucleophiles will generally proceed to Sn1 mechanism when a stable carbocation is present.  Below is a list of nucleophile trends in order of nucleophile strength.


We hope that this learning aid will help you answer any questions you may have had about Sn2 and Sn1 reactions. We here at StudyOrgo have compiled hundreds of reactions with clear explanations to help you speed up your studying and get a great grade in organic chemistry.  Sign up today to get access to all of our reactions!

How Are Radical Ions Formed?

Posted on August 28th, 2017

Many students taking Orgo 1 have commented there are a few types of reactions the professors save to the end of the semester and cover quickly and “gloss” over or sometimes skip all together in the interest of time.  However, in Orgo 2, you will be responsible for all of the reactions necessary for multi-step synthesis (starting product known to get to unknown final product) and retro-synthesis (product known to get to unknown starting material) reactions.  We at StudyOrgo don’t want you to get stuck on trying to cram for exams by studying reactions that were poorly covered in your class.

In this article we will review the steps to radical ion formation used in a few reaction including free radical halogenation of alkanes.  To begin, the three steps to radical reactions are 1) Initiation, 2) Propagation and finally 3) Termination.  The formation of radicals always occurs in the Propagation step of the reaction.  Energy has to be supplied to a molecule to induce a reaction known as homolytic cleavage; the breaking of a bond where both atoms receive 1 electron.  Most reactions occur by heterolytic cleavage, which means 2 electrons that formed the bond being broke are given to one atom (negative) while the other atom loses them (positive).

There are two methods for initiating radicals, either heat (symbolized as delta) or light (symbolized as hv).   To show the homolytic cleavage during initiation, the convention is to draw a fishhook arrow (one sided barb to the arrow) to each atom receiving one of the electrons.  In Orgo 1, you mechanisms will be graded on the quality of your fish-hook arrow and what bond the electrons came from to what atoms they are going towards, so be very clear!!!

Below is an example of heterolytic vs homolytic cleavage and how to draw the arrows correctly!

There are two other steps to free radical halogenation that occur.

Once the radical is created, it will attack alkane bonds (C-H) of substrate molecules to create H-X and a new radical alkane.  This step is referred to as propagation, since the radical is transferred from one molecule to the other essentially. To complete halogenation of the alkane, the radical alkane will attack the abundant halogen (e.g. Cl2, Br2) to form a new C-X bond and generate another radical halogen, just like from the initiation step.

The final step will be termination, where one radical attacks another and now a new bond is formed and no radical product is made.


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 and sign up today!