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Organic Chemistry for GAMSAT: where to start?

An area of GAMSAT Section III that people tend to get a little worried (or let’s just be honest, completely freak out!) about is Organic Chemistry.

In my opinion, with a good knowledge of the language of O-Chem, and good use of pattern recognition skills there’s no reason why most candidates can’t do really well on these questions. In fact, I’ve often said that organic chemistry gives you your best bang-for-buck when it comes to study to increase in GAMSAT score ratio.

So, here’s my three steps to getting a good start on Organic Chemistry questions.

1. Learn some basic functional groups.

I’m not a big fan of learning by rote, but having a small repertoire of functional groups at your disposal will definitely help with Organic Chemistry questions, in particular the speed at which you can digest and deconstruct the stimulus.

Check out these online functional groups flash cards to really nail it!

 Functional Groups Flashcards
Click to use the flashcards

 

It would be helpful if you knew how to draw and recognise the following functional groups: alkane, alkene, alcohol, aldehyde, ketone, carboxylic acid, ester, halide/haloalkane, amine, amide, benzene/aromatic ring. Those taking the cbsquared Chemistry course will find a summary of these functional groups including structural formula, condensed structural formula, name/common name, prefix/suffix and an example as a resource document.

 

2. Be able to name molecules using IUPAC nomenclature

Again, not a fan of rote learning, but you must be able to apply IUPAC nomenclature to name and draw molecules in order to answer questions quickly and effectively. The Organic Molecule Game (OMG) will really scare you into naming organic compounds quick smart. There’s a mad professor and a zombie to really increase the sense of urgency. Bonus.

OMG
Click to play
OMG mad professor
Click to get scared

 

3. Understand reaction maps and pathways to solve chemical reactions

This is where rote learning chemical reactions WILL NOT HELP YOU. You WILL receive a reaction that you’ve never seen before in the GAMSAT, probably with functional groups you’ve never seen before either. The trick is to be able to use pattern recognition skills to deconstruct the reaction given in the stimulus, and then apply to your particular example to get the answer.

For example, you’ll probably be given a general reaction sequence in the stimulus, then you’ll be asked to give the products of a similar reaction, with the same functional groups involved. You should then rewrite the general equation given, using your specific molecules, to ascertain the structure of the product. The basic backbone of the compound (or functional group) will be the same, here’s when you use your pattern recognition skills to recognise where the key functional group is, and how it has changed as a result of the reaction taking place.

Check out the “Master Organic Chemistry” site for a great blog post with some examples and work through. Below is a reaction pathways map from their blog, similar to what is included in the cbsquared Chemistry for GAMSAT course, in the resources section.

reaction-map2
Click to read the blog post

 

Please note: You will not be given a reaction pathways map in the GAMSAT. BUT you will be given a general reaction, or a few reactions, as part of the stimulus for the question. If you know how to use a reaction pathway map, you will also know how to use and interpret a reaction given to you in GAMSAT stimuli.

Good luck! If you need more practice, the cbsquared GAMSAT for Chemistry attendance or online course could be for you.

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Acids & Bases: a Guide to Tutorial 9 (Part 2)

This is the sequel to the post Acids & Bases: a Guide to Tutorial 9 Part 1.

See below for hints and tips and things you should know for questions 9.17-9.36.

Leo acidbase

Questions 9.17, 9.18, 9.19, 9.20, 9.21
Using equilibrium expressions for pKa to calculate pH and vice versa

  • Understand how to write equations for the dissociation of acids and bases with water. The general chemical equations are as follows:General equation of dissociation of an acid, HA in water:HA + H20 → A + H3O = KaGeneral equation of dissociation of a base, B in water:
    B + H20 → BH+ + OH = Kb
  • Know how to construct the equilibrium expressions for the above dissociation equations:Image result for acid dissociation constant    Understand that the concentrations of the species that we plug into the above expressions are the equilibrium concentrations after dissociation has occurred (not initial concentrations of acid or base)
  • Know or be able to derive the following equations:pH = -log[H+] and rearrange to:
    [H+] = 10-pH


    pOH = -log[OH]
    and rearrange to:
    [OH] = 10-pOH
    [H+][OH] = 1 x 10-14 and rearrange to:
    pH + pOH = 14
  • Be able to construct an equilibrium table (sometimes known as an ICE table or RICE chart, see here for an explanation) to show how concentrations change from initial to equilibrium concentrations
  • Understand the weak acid/base approximation-if you are told that the acid or base used is weak, then it will hardly dissociate at all. The initial concentration of acid or base will be pretty much the same at equilibrium. So we can approximate and make our calculations easier.
  • Equation used to calculate the percent ionisation of an acid or base:percentionisation

Step by step guide:

1. Write out the equation for the dissociation of the acid or base with water.

2. Ascertain what variable you need to calculate based on which of the following equilibrium expressions you will use:

Image result for acid dissociation constant or 
for example, you might be given the pH and therefore can calculate the Hconcentration, or you may be given the pKa and will need to convert this to the Ka.

3. Construct an ICE table in order to work out equilibrium concentrations.

4. Plug these values into one of the equilbrium expression equations above, you may need to rearrange and/or do a weak acid approximation in order to arrive at the value you need to answer the question.

5. Calcuate percent ionization if required using the equation shown earlier.

 

Questions 9.22 and 9.24
Acid strength as a result of molecular structure

  • Carboxylic acids are organic acids and are weak acids.
  • Be familiar with the 6 common strong acids:  hydrochloric acid (HCl), hydroiodic acid (HI), hydrobromic acid (HBr), perchloric acid (HClO4), nitric acid (HNO3) and sulfuric acid (H2SO4). These acids all ionize 100% in water. Know that anything that you come across that is not one of these strong acids is most likely a weak acid.
  • Understand how molecular structure affects acid strength. A general understanding of electronegativity and periodic trends would help here.
  • Benzoic acid is an organic acid with the carboxylic acid functional group, COOH. Boron and Fluorine are in the same period, so their acids, boric acid and hydrofluoric acid can be compared on the basis of the relative electronegativities of Fluorine and Boron. Fluorine is much more electronegative than Boron, so is a much stronger acid (although both are classed as weak acids).
  • Hydrofluoric acid, HF and iodic acid, HI are hydrogen halides, and their relative strength can be illustrated by the trend of acidity within the group 17 halogens. Unlike the trend for acidity across a period, the acidity down group 17 does not follow electronegativity. Iodic acid is the stronger acid of the two based on the poor orbital overlap due to size mismatch of the two atoms meaning that the H-X bond is weaker. This trend is discussed in the lecture notes for this topic.

 

Questions 9.23 and 9.25 – 9.28 and 9.30-9.32
Buffers and the Henderson-Hasselbalch equation

  • Know what a buffer is.
  • Be able to recognise and distinguish between acids, bases and their salt forms.
  • Understand how to use the Henderson-Hasselbalch equation:


Know that sometimes A is replaced with “base” and HA is replaced with “acid”
Keep in mind that when equal concentrations of acid and base are used, that it results in the entire last variable in the equation being “log 1” which is = 0.

Questions 9.29 and 9.33 – 9.36
Acid Base Titrations

  • Know the terms: equivalence point, half equivalence point, end point and be able to label them on a titration curve.
  • Know how to construct a titration curve (plot mL vs pH) and know roughly the different shapes depending on whether the titration involves a strong acid/strong base, strong acid/weak base or weak acid/strong base

 

Extra resources:

Check out the videos below from Crash Course and Khan Academy that summarise the concepts required for this tutorial.


Titration curves and acid-base indicators:

 

For more information about how the cbsquared Chemistry for GAMSAT course can help you achieve your GAMSAT and medical school goals, or just for some guidance and advice about how to kick start your study, please feel free to get in touch.

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Handy reference: List of ions, orbitals, equations & constants

When you’re getting started with Chemistry, the volume of information thrown at you can seem overwhelming.

Students taking the cbsquared Chemistry for GAMSAT course have a host of resource documents available to them in the course already, but I thought I would post a few extra online resources with a few great images to help you form a visual picture of the building blocks of chemistry at the molecular level.

Please note: here is no need to rote learn any of this material for the GAMSAT!

1. Table of common polyatomic ions with 3D models.

Once you get to topic 2 and 3, we start talking about lewis dot structures and it can be helpful to be familiar with some common polyatomic ions.

Polyatomic ions table

 

 

2. Orbitron, a website with images showing what the orbitals and hybridised orbitals look like in 3D

Useful for understanding what an atomic orbital might look like, and also for the hybridisation topic, to get an idea of what hybrid orbitals look like.

Orbitron

 

 

3. Lists of useful equations and physical constants used in physical chemistry.*

*PLEASE NOTE: You do not need to rote learn these equations or physical constants. They will be provided in the stimulus of the GAMSAT question. You should learn the very basic equations, such as c = n/v and n = m/M for chemistry questions.

For more information about how the cbsquared Chemistry for GAMSAT course can help you achieve your GAMSAT and medical school goals, or just for some guidance and advice about how to kick start your study, please feel free to get in touch.

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Making maths in physical chemistry less scary

Once students arrive at the physical chemistry topics of the Chemistry for GAMSAT course, they are confronted with a subset of mathematical skills that are required.

The maths is quite straight forward believe it or not, but the big equations and the use of logarithms can make these questions seem more difficult, and let’s face it, sometimes kinda scary!

Fear not, it takes a little practice but the more you see and use your basic math skills with these equations, the less scary they become, until you’re laughing in the face of huge equations!

The following set of videos cover the following mathematical techniques:

  • Rearranging equations involving logs
  • Using simultaneous equations to find values for more than one unknown
  • “Linearising” an equation (ready for graphing, or just to simplify)

The idea of this post is to remove some of the “scary factor” when you see complex equations, and to help you become more familiar with, and learn how to manipulate them.

All the videos are around 3 minutes long. If you don’t understand the rearragements or log rules, you should consult the other maths for Chemistry resources on this blog, such as “Logs in less than 5 minutes“.

Resource 1: Logarithms in Chemical calculations

The following resource explains the maths used when manipulating some common physical chemistry equations.

  • Nernst Equation: The use of log to base 10 and the natural log (ln) in the Nernst equation is shown, and how the equation can be rearranged to be able to plot on a straight line graph.
  • Gibbs Free energy related to the Equilibrium Constant: How to rearrange the equation ΔG = RTlnK to solve for using log rules
  • Clausius-Clapeyron Equation (relating vapour pressure to temperature): Another example of how to rearrange an equation involving log rules.

Resource 2: Simultaneous Equations and the Arrhenius Equation

This video is concerned with the Arrhenius equation (relates the rate constant k to the temperature). It summarises the following:

  • Rearranging the Arrhenius equation into a “linear” form
  • Using simultaneous equations to solve for more than one unknown

Resource 3: Simultaneous Equations and Thermodynamic Expressions

More practice at using simultaneous equations and rearranging equations with logs in them.

I hope these resources help you feel more at ease with some scary looking equations.

For more information about cbsquared GAMSAT preparation courses, please visit: https://cbsquared.co/learn/courses/

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i.o.u. an explanation for a.m.u.

Ok, let’s get something straight.

There’s a lot of language to get your head around when you first start out with Chemistry, and it all starts with how the very smallest chemical particle is measured.

In topic 1 of the Chemistry for GAMSAT course, we start from the very basics, so this post is to help you get off to a good start.

It’s the small things….

We are dealing with such small particles, that have very very small masses, so there are some unique terms that have been derived to help us. It will help if you have an understanding of the following terms:

  • atomic mass
  • relative atomic mass (replaces the old term atomic weight)
  • unified atomic mass unit (replaces the old term atomic mass unit)

The following video has a good introduction from first principles, including a quick explanation of the distinction that physicists make between weight and mass. The chemistry definitions start around the three minute mark.

 

Notice that the video makes no mention of relative atomic mass, or of unified atomic mass unit, which are actually the new terms for the atomic weight and the atomic mass unit respectively.

Although still somewhat shrouded in controversy among chemists, the terms relative atomic mass and unified atomic mass unit (still abbreviated to amu) replace the old terms. However, both terms in each case are still in use and are officially sanctioned by the International Union of Pure and Applied Chemistry (IUPAC)

Out with the old, in with the new:

  • The relative atomic mass is exactly equivalent to the old term atomic weight. Changed in 1961 after controversey arising from the distinction between weight and mass.
  • The unified atomic mass unit is the new term for atomic mass unit, both are abbrevieated to amu.

What does it all mean?

unified atomic mass unit

  • Defined 112 of the mass of an atom of carbon-12.
  • Symbol u.
  • One unified atomic mass unit is approximately the mass of one proton (or one neutron) and is equivalent to 1 g/mol.
  • Has a value of 1.660538921(73)×10−27 kg.

relative atomic mass 

  • Defined as m/mu where m is the average mass of an element and mu is atomic mass constant. (mu = m(12C)/12 which = 1 Da or 1 u).
  • Symbol Ar.
  • This is the number that appears on the periodic table which takes into account natural isotopic abundances.
  • Indicates a ratio-it compares a property of one substance to the same property of another substance. Hence it has no units, it is strictly not a mass but a ratio of two masses.
  • However, for both practical and historical reasons, relative atomic masses (and molecular masses) are almost always quoted in grams per mole (g/mol or g mol−1) in chemistry.

atomic mass

  • Defined as the mass of an atomic particle, sub-atomic particle, or molecule.
  • Symbol ma
  • Commonly expressed in unified atomic mass units (u)
  • Does not take into account natural isotopic abundances.

For another explanation of the atomic mass units, relative atomic mass and natural isotopic abundance, check out the Fuse School videos below:

This is covered in Tutorial 1 of the Chemistry for GAMSAT course. To view a preview of the course click here.

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